diff --git a/app/controllers/projects/issues_controller.rb b/app/controllers/projects/issues_controller.rb
index 0ac9da2ff0f..e2ccabb22db 100644
--- a/app/controllers/projects/issues_controller.rb
+++ b/app/controllers/projects/issues_controller.rb
@@ -8,7 +8,6 @@ class Projects::IssuesController < Projects::ApplicationController
 
   prepend_before_action :authenticate_user!, only: [:new]
 
-  before_action :redirect_to_external_issue_tracker, only: [:index, :new]
   before_action :check_issues_available!
   before_action :issue, except: [:index, :new, :create, :bulk_update]
 
@@ -243,19 +242,19 @@ class Projects::IssuesController < Projects::ApplicationController
   end
 
   def authorize_update_issue!
-    return render_404 unless can?(current_user, :update_issue, @issue)
+    render_404 unless can?(current_user, :update_issue, @issue)
   end
 
   def authorize_admin_issues!
-    return render_404 unless can?(current_user, :admin_issue, @project)
+    render_404 unless can?(current_user, :admin_issue, @project)
   end
 
   def authorize_create_merge_request!
-    return render_404 unless can?(current_user, :push_code, @project) && @issue.can_be_worked_on?(current_user)
+    render_404 unless can?(current_user, :push_code, @project) && @issue.can_be_worked_on?(current_user)
   end
 
   def check_issues_available!
-    return render_404 unless @project.feature_available?(:issues, current_user) && @project.default_issues_tracker?
+    return render_404 unless @project.feature_available?(:issues, current_user)
   end
 
   def redirect_to_external_issue_tracker
diff --git a/app/helpers/issues_helper.rb b/app/helpers/issues_helper.rb
index 42b6cfdf02f..7e1ccb23e9e 100644
--- a/app/helpers/issues_helper.rb
+++ b/app/helpers/issues_helper.rb
@@ -17,10 +17,10 @@ module IssuesHelper
     return '' if project.nil?
 
     url =
-      if options[:only_path]
-        project.issues_tracker.issue_path(issue_iid)
+      if options[:internal]
+        url_for_internal_issue(issue_iid, project, options)
       else
-        project.issues_tracker.issue_url(issue_iid)
+        url_for_tracker_issue(issue_iid, project, options)
       end
 
     # Ensure we return a valid URL to prevent possible XSS.
@@ -29,6 +29,24 @@ module IssuesHelper
     ''
   end
 
+  def url_for_tracker_issue(issue_iid, project, options)
+    if options[:only_path]
+      project.issues_tracker.issue_path(issue_iid)
+    else
+      project.issues_tracker.issue_url(issue_iid)
+    end
+  end
+
+  def url_for_internal_issue(issue_iid, project = @project, options = {})
+    helpers = Gitlab::Routing.url_helpers
+
+    if options[:only_path]
+      helpers.namespace_project_issue_path(namespace_id: project.namespace, project_id: project, id: issue_iid)
+    else
+      helpers.namespace_project_issue_url(namespace_id: project.namespace, project_id: project, id: issue_iid)
+    end
+  end
+
   def bulk_update_milestone_options
     milestones = @project.milestones.active.reorder(due_date: :asc, title: :asc).to_a
     milestones.unshift(Milestone::None)
@@ -158,4 +176,6 @@ module IssuesHelper
 
   # Required for Banzai::Filter::IssueReferenceFilter
   module_function :url_for_issue
+  module_function :url_for_internal_issue
+  module_function :url_for_tracker_issue
 end
diff --git a/app/models/merge_request.rb b/app/models/merge_request.rb
index e4e7999d0f2..a910099b4c1 100644
--- a/app/models/merge_request.rb
+++ b/app/models/merge_request.rb
@@ -596,7 +596,7 @@ class MergeRequest < ActiveRecord::Base
   # running `ReferenceExtractor` on each of them separately.
   # This optimization does not apply to issues from external sources.
   def cache_merge_request_closes_issues!(current_user)
-    return if project.has_external_issue_tracker?
+    return unless project.issues_enabled?
 
     transaction do
       self.merge_requests_closing_issues.delete_all
diff --git a/app/models/project.rb b/app/models/project.rb
index 0b357d5d003..d827bfaa806 100644
--- a/app/models/project.rb
+++ b/app/models/project.rb
@@ -734,9 +734,11 @@ class Project < ActiveRecord::Base
   end
 
   def get_issue(issue_id, current_user)
-    if default_issues_tracker?
-      IssuesFinder.new(current_user, project_id: id).find_by(iid: issue_id)
-    else
+    issue = IssuesFinder.new(current_user, project_id: id).find_by(iid: issue_id) if issues_enabled?
+
+    if issue
+      issue
+    elsif external_issue_tracker
       ExternalIssue.new(issue_id, self)
     end
   end
@@ -758,7 +760,7 @@ class Project < ActiveRecord::Base
   end
 
   def external_issue_reference_pattern
-    external_issue_tracker.class.reference_pattern
+    external_issue_tracker.class.reference_pattern(only_long: issues_enabled?)
   end
 
   def default_issues_tracker?
diff --git a/app/models/project_services/issue_tracker_service.rb b/app/models/project_services/issue_tracker_service.rb
index 6d6a3ae3647..31984c5d7ed 100644
--- a/app/models/project_services/issue_tracker_service.rb
+++ b/app/models/project_services/issue_tracker_service.rb
@@ -8,8 +8,12 @@ class IssueTrackerService < Service
   # This pattern does not support cross-project references
   # The other code assumes that this pattern is a superset of all
   # overriden patterns. See ReferenceRegexes::EXTERNAL_PATTERN
-  def self.reference_pattern
-    @reference_pattern ||= %r{(\b[A-Z][A-Z0-9_]+-|#{Issue.reference_prefix})(?<issue>\d+)}
+  def self.reference_pattern(only_long: false)
+    if only_long
+      %r{(\b[A-Z][A-Z0-9_]+-)(?<issue>\d+)}
+    else
+      %r{(\b[A-Z][A-Z0-9_]+-|#{Issue.reference_prefix})(?<issue>\d+)}
+    end
   end
 
   def default?
diff --git a/app/models/project_services/jira_service.rb b/app/models/project_services/jira_service.rb
index 5498a2e17b2..450027c2e57 100644
--- a/app/models/project_services/jira_service.rb
+++ b/app/models/project_services/jira_service.rb
@@ -18,7 +18,7 @@ class JiraService < IssueTrackerService
   end
 
   # {PROJECT-KEY}-{NUMBER} Examples: JIRA-1, PROJECT-1
-  def self.reference_pattern
+  def self.reference_pattern(only_long: true)
     @reference_pattern ||= %r{(?<issue>\b([A-Z][A-Z0-9_]+-)\d+)}
   end
 
diff --git a/app/policies/project_policy.rb b/app/policies/project_policy.rb
index 323131c0f7e..d27bbf2948c 100644
--- a/app/policies/project_policy.rb
+++ b/app/policies/project_policy.rb
@@ -287,9 +287,6 @@ class ProjectPolicy < BasePolicy
     prevent :create_issue
     prevent :update_issue
     prevent :admin_issue
-  end
-
-  rule { issues_disabled & default_issues_tracker }.policy do
     prevent :read_issue
   end
 
diff --git a/app/services/issues/close_service.rb b/app/services/issues/close_service.rb
index ddef5281498..74459c3342c 100644
--- a/app/services/issues/close_service.rb
+++ b/app/services/issues/close_service.rb
@@ -16,13 +16,13 @@ module Issues
     # The code calling this method is responsible for ensuring that a user is
     # allowed to close the given issue.
     def close_issue(issue, commit: nil, notifications: true, system_note: true)
-      if project.jira_tracker? && project.jira_service.active
+      if project.jira_tracker? && project.jira_service.active && issue.is_a?(ExternalIssue)
         project.jira_service.close_issue(commit, issue)
         todo_service.close_issue(issue, current_user)
         return issue
       end
 
-      if project.default_issues_tracker? && issue.close
+      if project.issues_enabled? && issue.close
         event_service.close_issue(issue, current_user)
         create_note(issue, commit) if system_note
         notification_service.close_issue(issue, current_user) if notifications
diff --git a/app/views/layouts/nav/_new_project_sidebar.html.haml b/app/views/layouts/nav/_new_project_sidebar.html.haml
index 21f175291fa..00395b222e4 100644
--- a/app/views/layouts/nav/_new_project_sidebar.html.haml
+++ b/app/views/layouts/nav/_new_project_sidebar.html.haml
@@ -75,10 +75,10 @@
             Registry
 
     - if project_nav_tab? :issues
-      = nav_link(controller: @project.default_issues_tracker? ? [:issues, :labels, :milestones, :boards] : :issues) do
+      = nav_link(controller: @project.issues_enabled? ? [:issues, :labels, :milestones, :boards] : :issues) do
         = link_to project_issues_path(@project), title: 'Issues', class: 'shortcuts-issues' do
           %span
-            - if @project.default_issues_tracker?
+            - if @project.issues_enabled?
               %span.badge.count.issue_counter= number_with_delimiter(IssuesFinder.new(current_user, project_id: @project.id).execute.opened.count)
             Issues
 
@@ -113,7 +113,7 @@
                   Milestones
 
     - if project_nav_tab? :merge_requests
-      = nav_link(controller: @project.default_issues_tracker? ? :merge_requests : [:merge_requests, :labels, :milestones]) do
+      = nav_link(controller: @project.issues_enabled? ? :merge_requests : [:merge_requests, :labels, :milestones]) do
         = link_to project_merge_requests_path(@project), title: 'Merge Requests', class: 'shortcuts-merge_requests' do
           %span
             %span.badge.count.merge_counter.js-merge-counter= number_with_delimiter(MergeRequestsFinder.new(current_user, project_id: @project.id).execute.opened.count)
diff --git a/app/views/layouts/nav/_project.html.haml b/app/views/layouts/nav/_project.html.haml
index fb90bb4b472..924cd2e9681 100644
--- a/app/views/layouts/nav/_project.html.haml
+++ b/app/views/layouts/nav/_project.html.haml
@@ -23,16 +23,16 @@
             Registry
 
     - if project_nav_tab? :issues
-      = nav_link(controller: @project.default_issues_tracker? ? [:issues, :labels, :milestones, :boards] : :issues) do
+      = nav_link(controller: @project.issues_enabled? ? [:issues, :labels, :milestones, :boards] : :issues) do
         = link_to project_issues_path(@project), title: 'Issues', class: 'shortcuts-issues' do
           %span
             Issues
-            - if @project.default_issues_tracker?
+            - if @project.issues_enabled?
               %span.badge.count.issue_counter= number_with_delimiter(issuables_count_for_state(:issues, :opened, finder: IssuesFinder.new(current_user, project_id: @project.id)))
 
     - if project_nav_tab? :merge_requests
       - controllers = [:merge_requests, 'projects/merge_requests/conflicts']
-      - controllers.push(:merge_requests, :labels, :milestones) unless @project.default_issues_tracker?
+      - controllers.push(:merge_requests, :labels, :milestones) unless @project.issues_enabled?
       = nav_link(controller: controllers) do
         = link_to project_merge_requests_path(@project), title: 'Merge Requests', class: 'shortcuts-merge_requests' do
           %span
diff --git a/app/views/projects/merge_requests/index.html.haml b/app/views/projects/merge_requests/index.html.haml
index bfeb746ee83..c020e7db380 100644
--- a/app/views/projects/merge_requests/index.html.haml
+++ b/app/views/projects/merge_requests/index.html.haml
@@ -4,7 +4,7 @@
 - new_merge_request_path = project_new_merge_request_path(merge_project) if merge_project
 
 - page_title "Merge Requests"
-- unless @project.default_issues_tracker?
+- unless @project.issues_enabled?
   = content_for :sub_nav do
     = render "projects/merge_requests/head"
 
diff --git a/app/views/shared/_mr_head.html.haml b/app/views/shared/_mr_head.html.haml
index 4211ec6351d..e7355ae2eea 100644
--- a/app/views/shared/_mr_head.html.haml
+++ b/app/views/shared/_mr_head.html.haml
@@ -1,4 +1,4 @@
-- if @project.default_issues_tracker?
+- if @project.issues_enabled?
   = render "projects/issues/head"
 - else
   = render "projects/merge_requests/head"
diff --git a/changelogs/unreleased/33097-issue-tracker.yml b/changelogs/unreleased/33097-issue-tracker.yml
new file mode 100644
index 00000000000..0b13f7165db
--- /dev/null
+++ b/changelogs/unreleased/33097-issue-tracker.yml
@@ -0,0 +1,4 @@
+---
+title: Associate Issues tab only with internal issues tracker
+merge_request:
+author:
diff --git a/doc/integration/external-issue-tracker.md b/doc/integration/external-issue-tracker.md
index 2dd9b33273c..372e1909330 100644
--- a/doc/integration/external-issue-tracker.md
+++ b/doc/integration/external-issue-tracker.md
@@ -4,14 +4,12 @@ GitLab has a great issue tracker but you can also use an external one such as
 Jira, Redmine, or Bugzilla. Issue trackers are configurable per GitLab project and allow
 you to do the following:
 
-- the **Issues** link on the GitLab project pages takes you to the appropriate
-  issue index of the external tracker
-- clicking **New issue** on the project dashboard creates a new issue on the
-  external tracker
 - you can reference these external issues inside GitLab interface
   (merge requests, commits, comments) and they will be automatically converted
   into links
 
+You can have enabled both external and internal GitLab issue trackers in parallel. The **Issues** link always opens the internal issue tracker and in case the internal issue tracker is disabled the link is not visible in the menu.
+
 ## Configuration
 
 The configuration is done via a project's **Services**.
diff --git a/doc/user/project/integrations/bugzilla.md b/doc/user/project/integrations/bugzilla.md
index 6a040516231..ba2adc1afda 100644
--- a/doc/user/project/integrations/bugzilla.md
+++ b/doc/user/project/integrations/bugzilla.md
@@ -20,10 +20,12 @@ Once you have configured and enabled Bugzilla:
 ## Referencing issues in Bugzilla
 
 Issues in Bugzilla can be referenced in two alternative ways:
-1. `#<ID>` where `<ID>` is a number (example `#143`)
+1. `#<ID>` where `<ID>` is a number (example `#143`).
 2. `<PROJECT>-<ID>` where `<PROJECT>` starts with a capital letter which is
   then followed by capital letters, numbers or underscores, and `<ID>` is
   a number (example `API_32-143`).
 
+We suggest using the longer format if you have both internal and external issue trackers enabled. If you use the shorter format and an issue with the same ID exists in the internal issue tracker the internal issue will be linked.
+
 Please note that `<PROJECT>` part is ignored and links always point to the
 address specified in `issues_url`.
diff --git a/doc/user/project/integrations/redmine.md b/doc/user/project/integrations/redmine.md
index 8026f1f57bc..cf92465da53 100644
--- a/doc/user/project/integrations/redmine.md
+++ b/doc/user/project/integrations/redmine.md
@@ -30,5 +30,7 @@ Issues in Redmine can be referenced in two alternative ways:
   then followed by capital letters, numbers or underscores, and `<ID>` is
   a number (example `API_32-143`).
 
+We suggest using the longer format if you have both internal and external issue trackers enabled. If you use the shorter format and an issue with the same ID exists in the internal issue tracker the internal issue will be linked.
+
 Please note that `<PROJECT>` part is ignored and links always point to the
 address specified in `issues_url`.
diff --git a/lib/api/entities.rb b/lib/api/entities.rb
index 09a88869063..1719e9f7205 100644
--- a/lib/api/entities.rb
+++ b/lib/api/entities.rb
@@ -109,7 +109,7 @@ module API
         user.avatar_url(only_path: false)
       end
       expose :star_count, :forks_count
-      expose :open_issues_count, if: lambda { |project, options| project.feature_available?(:issues, options[:current_user]) && project.default_issues_tracker? }
+      expose :open_issues_count, if: lambda { |project, options| project.feature_available?(:issues, options[:current_user]) }
       expose :runners_token, if: lambda { |_project, options| options[:user_can_admin_project] }
       expose :public_builds, as: :public_jobs
       expose :ci_config_path
diff --git a/lib/api/merge_requests.rb b/lib/api/merge_requests.rb
index 6e2e13e0a24..f64ac659413 100644
--- a/lib/api/merge_requests.rb
+++ b/lib/api/merge_requests.rb
@@ -29,14 +29,6 @@ module API
           render_api_error!(errors, 400)
         end
 
-        def issue_entity(project)
-          if project.has_external_issue_tracker?
-            Entities::ExternalIssue
-          else
-            Entities::IssueBasic
-          end
-        end
-
         def find_merge_requests(args = {})
           args = params.merge(args)
 
@@ -278,7 +270,14 @@ module API
       get ':id/merge_requests/:merge_request_iid/closes_issues' do
         merge_request = find_merge_request_with_access(params[:merge_request_iid])
         issues = ::Kaminari.paginate_array(merge_request.closes_issues(current_user))
-        present paginate(issues), with: issue_entity(user_project), current_user: current_user
+        issues = paginate(issues)
+
+        external_issues, internal_issues = issues.partition { |issue| issue.is_a?(ExternalIssue) }
+
+        data = Entities::IssueBasic.represent(internal_issues, current_user: current_user)
+        data += Entities::ExternalIssue.represent(external_issues, current_user: current_user)
+
+        data.as_json
       end
     end
   end
diff --git a/lib/banzai/filter/issue_reference_filter.rb b/lib/banzai/filter/issue_reference_filter.rb
index ba1a5ac84b3..ce1ab977d3b 100644
--- a/lib/banzai/filter/issue_reference_filter.rb
+++ b/lib/banzai/filter/issue_reference_filter.rb
@@ -20,7 +20,7 @@ module Banzai
       end
 
       def url_for_object(issue, project)
-        IssuesHelper.url_for_issue(issue.iid, project, only_path: context[:only_path])
+        IssuesHelper.url_for_issue(issue.iid, project, only_path: context[:only_path], internal: true)
       end
 
       def project_from_ref(ref)
diff --git a/lib/banzai/reference_parser/external_issue_parser.rb b/lib/banzai/reference_parser/external_issue_parser.rb
index 6307c1b571a..1802cd04854 100644
--- a/lib/banzai/reference_parser/external_issue_parser.rb
+++ b/lib/banzai/reference_parser/external_issue_parser.rb
@@ -21,10 +21,14 @@ module Banzai
         gather_attributes_per_project(nodes, self.class.data_attribute)
       end
 
-      private
-
+      # we extract only external issue trackers references here, we don't extract cross-project references,
+      # so we don't need to do anything here.
       def can_read_reference?(user, ref_project, node)
-        can?(user, :read_issue, ref_project)
+        true
+      end
+
+      def nodes_visible_to_user(user, nodes)
+        nodes
       end
     end
   end
diff --git a/lib/gitlab/reference_extractor.rb b/lib/gitlab/reference_extractor.rb
index 7668ecacc4b..f5b757ace77 100644
--- a/lib/gitlab/reference_extractor.rb
+++ b/lib/gitlab/reference_extractor.rb
@@ -33,7 +33,12 @@ module Gitlab
 
     def issues
       if project && project.jira_tracker?
-        @references[:external_issue] ||= references(:external_issue)
+        if project.issues_enabled?
+          @references[:all_issues] ||= references(:external_issue) + references(:issue)
+        else
+          @references[:external_issue] ||= references(:external_issue) +
+            references(:issue).select { |i| i.project_id != project.id }
+        end
       else
         @references[:issue] ||= references(:issue)
       end
diff --git a/lib/gitlab/slash_commands/issue_command.rb b/lib/gitlab/slash_commands/issue_command.rb
index 87ea19b8806..3d96982b820 100644
--- a/lib/gitlab/slash_commands/issue_command.rb
+++ b/lib/gitlab/slash_commands/issue_command.rb
@@ -2,7 +2,7 @@ module Gitlab
   module SlashCommands
     class IssueCommand < BaseCommand
       def self.available?(project)
-        project.issues_enabled? && project.default_issues_tracker?
+        project.issues_enabled?
       end
 
       def collection
diff --git a/spec/controllers/projects/issues_controller_spec.rb b/spec/controllers/projects/issues_controller_spec.rb
index 18d0be3c103..e56f5d11daf 100644
--- a/spec/controllers/projects/issues_controller_spec.rb
+++ b/spec/controllers/projects/issues_controller_spec.rb
@@ -7,16 +7,30 @@ describe Projects::IssuesController do
 
   describe "GET #index" do
     context 'external issue tracker' do
-      let!(:service) do
-        create(:custom_issue_tracker_service, project: project, title: 'Custom Issue Tracker', project_url: 'http://test.com')
+      before do
+        sign_in(user)
+        project.add_developer(user)
+        create(:jira_service, project: project)
       end
 
-      it 'redirects to the external issue tracker' do
-        controller.instance_variable_set(:@project, project)
+      context 'when GitLab issues disabled' do
+        it 'returns 404 status' do
+          project.issues_enabled = false
+          project.save!
 
-        get :index, namespace_id: project.namespace, project_id: project
+          get :index, namespace_id: project.namespace, project_id: project
 
-        expect(response).to redirect_to(service.issue_tracker_path)
+          expect(response).to have_http_status(404)
+        end
+      end
+
+      context 'when GitLab issues enabled' do
+        it 'renders the "index" template' do
+          get :index, namespace_id: project.namespace, project_id: project
+
+          expect(response).to have_http_status(200)
+          expect(response).to render_template(:index)
+        end
       end
     end
 
@@ -42,15 +56,7 @@ describe Projects::IssuesController do
 
       it "returns 404 when issues are disabled" do
         project.issues_enabled = false
-        project.save
-
-        get :index, namespace_id: project.namespace, project_id: project
-        expect(response).to have_http_status(404)
-      end
-
-      it "returns 404 when external issue tracker is enabled" do
-        controller.instance_variable_set(:@project, project)
-        allow(project).to receive(:default_issues_tracker?).and_return(false)
+        project.save!
 
         get :index, namespace_id: project.namespace, project_id: project
         expect(response).to have_http_status(404)
@@ -148,14 +154,29 @@ describe Projects::IssuesController do
       before do
         sign_in(user)
         project.team << [user, :developer]
+
+        external = double
+        allow(project).to receive(:external_issue_tracker).and_return(external)
       end
 
-      it 'redirects to the external issue tracker' do
-        controller.instance_variable_set(:@project, project)
+      context 'when GitLab issues disabled' do
+        it 'returns 404 status' do
+          project.issues_enabled = false
+          project.save!
 
-        get :new, namespace_id: project.namespace, project_id: project
+          get :new, namespace_id: project.namespace, project_id: project
 
-        expect(response).to redirect_to('http://test.com')
+          expect(response).to have_http_status(404)
+        end
+      end
+
+      context 'when GitLab issues enabled' do
+        it 'renders the "new" template' do
+          get :new, namespace_id: project.namespace, project_id: project
+
+          expect(response).to have_http_status(200)
+          expect(response).to render_template(:new)
+        end
       end
     end
   end
diff --git a/spec/features/issuables/markdown_references_spec.rb b/spec/features/issuables/markdown_references_spec.rb
new file mode 100644
index 00000000000..f51b2e4001a
--- /dev/null
+++ b/spec/features/issuables/markdown_references_spec.rb
@@ -0,0 +1,193 @@
+require 'rails_helper'
+
+describe 'Markdown References', :feature, :js do
+  let(:user)    { create(:user) }
+  let(:actual_project) { create(:project, :public) }
+  let(:merge_request) { create(:merge_request, target_project: actual_project, source_project: actual_project)}
+  let(:issue_actual_project) { create(:issue, project: actual_project) }
+  let!(:other_project) { create(:empty_project, :public) }
+  let!(:issue_other_project)   { create(:issue, project: other_project) }
+  let(:issues) { [issue_actual_project, issue_other_project] }
+
+  def build_note
+    markdown = "Referencing internal issue #{issue_actual_project.to_reference}, " +
+      "cross-project #{issue_other_project.to_reference(actual_project)} external JIRA-5 " +
+      "and non existing #999"
+
+    page.within('#diff-notes-app') do
+      fill_in 'note_note', with: markdown
+    end
+  end
+
+  shared_examples 'correct references' do
+    before do
+      remotelink = double(:remotelink, all: [], build: double(save!: true))
+
+      stub_request(:get, "https://jira.example.com/rest/api/2/issue/JIRA-5")
+      stub_request(:post, "https://jira.example.com/rest/api/2/issue/JIRA-5/comment")
+      allow_any_instance_of(JIRA::Resource::Issue).to receive(:remotelink).and_return(remotelink)
+
+      sign_in(user)
+      visit merge_request_path(merge_request)
+      build_note
+    end
+
+    def links_expectations
+      issues.each do |issue|
+        if referenced_issues.include?(issue)
+          expect(page).to have_link(issue.to_reference, href: issue_path(issue))
+        else
+          expect(page).not_to have_link(issue.to_reference, href: issue_path(issue))
+        end
+      end
+
+      if jira_referenced
+        expect(page).to have_link('JIRA-5', href: 'https://jira.example.com/browse/JIRA-5')
+      else
+        expect(page).not_to have_link('JIRA-5', href: 'https://jira.example.com/browse/JIRA-5')
+      end
+
+      expect(page).not_to have_link('#999')
+    end
+
+    it 'creates a link to the referenced issue on the preview' do
+      find('.js-md-preview-button').click
+      wait_for_requests
+
+      page.within('.md-preview-holder') do
+        links_expectations
+      end
+    end
+
+    it 'creates a link to the referenced issue after submit' do
+      click_button 'Comment'
+      wait_for_requests
+
+      page.within('#diff-notes-app') do
+        links_expectations
+      end
+    end
+
+    it 'creates a note on the referenced issues' do
+      click_button 'Comment'
+      wait_for_requests
+
+      if referenced_issues.include?(issue_actual_project)
+        visit issue_path(issue_actual_project)
+
+        page.within('#notes') do
+          expect(page).to have_content(
+            "#{user.to_reference} mentioned in merge request #{merge_request.to_reference}"
+          )
+        end
+      end
+
+      if referenced_issues.include?(issue_other_project)
+        visit issue_path(issue_other_project)
+
+        page.within('#notes') do
+          expect(page).to have_content(
+            "#{user.to_reference} mentioned in merge request #{merge_request.to_reference(other_project)}"
+          )
+        end
+      end
+    end
+  end
+
+  context 'when internal issues tracker is enabled for the other project' do
+    context 'when only internal issues tracker is enabled for the actual project' do
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_actual_project, issue_other_project] }
+        let(:jira_referenced)   { false }
+      end
+    end
+
+    context 'when both external and internal issues trackers are enabled for the actual project' do
+      before do
+        create(:jira_service, project: actual_project)
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_actual_project, issue_other_project] }
+        let(:jira_referenced)   { true }
+      end
+    end
+
+    context 'when only external issues tracker is enabled for the actual project' do
+      before do
+        create(:jira_service, project: actual_project)
+
+        actual_project.issues_enabled = false
+        actual_project.save!
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_other_project] }
+        let(:jira_referenced)   { true }
+      end
+    end
+
+    context 'when no tracker is enabled for the actual project' do
+      before do
+        actual_project.issues_enabled = false
+        actual_project.save!
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_other_project] }
+        let(:jira_referenced)   { false }
+      end
+    end
+  end
+
+  context 'when internal issues tracker is disabled for the other project' do
+    before do
+      other_project.issues_enabled = false
+      other_project.save!
+    end
+
+    context 'when only internal issues tracker is enabled for the actual project' do
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_actual_project] }
+        let(:jira_referenced)   { false }
+      end
+    end
+
+    context 'when both external and internal issues trackers are enabled for the actual project' do
+      before do
+        create(:jira_service, project: actual_project)
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_actual_project] }
+        let(:jira_referenced)   { true }
+      end
+    end
+
+    context 'when only external issues tracker is enabled for the actual project' do
+      before do
+        create(:jira_service, project: actual_project)
+
+        actual_project.issues_enabled = false
+        actual_project.save!
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [] }
+        let(:jira_referenced)   { true }
+      end
+    end
+
+    context 'when no issues tracker is enabled for the actual project' do
+      before do
+        actual_project.issues_enabled = false
+        actual_project.save!
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [] }
+        let(:jira_referenced)   { false }
+      end
+    end
+  end
+end
diff --git a/spec/features/projects/features_visibility_spec.rb b/spec/features/projects/features_visibility_spec.rb
index 827e02a58d0..1588f8a828a 100644
--- a/spec/features/projects/features_visibility_spec.rb
+++ b/spec/features/projects/features_visibility_spec.rb
@@ -39,14 +39,25 @@ describe 'Edit Project Settings', feature: true do
       end
     end
 
-    context "When external issue tracker is enabled" do
-      it "does not hide issues tab" do
-        project.project_feature.update(issues_access_level: ProjectFeature::DISABLED)
+    context 'When external issue tracker is enabled and issues enabled on project settings' do
+      it 'does not hide issues tab' do
         allow_any_instance_of(Project).to receive(:external_issue_tracker).and_return(JiraService.new)
 
         visit project_path(project)
 
-        expect(page).to have_selector(".shortcuts-issues")
+        expect(page).to have_selector('.shortcuts-issues')
+      end
+    end
+
+    context 'When external issue tracker is enabled and issues disabled on project settings' do
+      it 'hides issues tab' do
+        project.issues_enabled = false
+        project.save!
+        allow_any_instance_of(Project).to receive(:external_issue_tracker).and_return(JiraService.new)
+
+        visit project_path(project)
+
+        expect(page).not_to have_selector('.shortcuts-issues')
       end
     end
 
diff --git a/spec/helpers/issues_helper_spec.rb b/spec/helpers/issues_helper_spec.rb
index 8f7f17a484f..9524a101e74 100644
--- a/spec/helpers/issues_helper_spec.rb
+++ b/spec/helpers/issues_helper_spec.rb
@@ -8,7 +8,7 @@ describe IssuesHelper do
   describe "url_for_issue" do
     let(:issues_url) { ext_project.external_issue_tracker.issues_url}
     let(:ext_expected) { issues_url.gsub(':id', issue.iid.to_s).gsub(':project_id', ext_project.id.to_s) }
-    let(:int_expected) { polymorphic_path([@project.namespace, project, issue]) }
+    let(:int_expected) { polymorphic_path([@project.namespace, @project, issue]) }
 
     it "returns internal path if used internal tracker" do
       @project = project
@@ -22,6 +22,12 @@ describe IssuesHelper do
       expect(url_for_issue(issue.iid)).to match(ext_expected)
     end
 
+    it "returns path to internal issue when internal option passed" do
+      @project = ext_project
+
+      expect(url_for_issue(issue.iid, ext_project, internal: true)).to match(int_expected)
+    end
+
     it "returns empty string if project nil" do
       @project = nil
 
diff --git a/spec/lib/banzai/filter/external_issue_reference_filter_spec.rb b/spec/lib/banzai/filter/external_issue_reference_filter_spec.rb
index b7d82c36ddd..fb320e0148a 100644
--- a/spec/lib/banzai/filter/external_issue_reference_filter_spec.rb
+++ b/spec/lib/banzai/filter/external_issue_reference_filter_spec.rb
@@ -108,6 +108,11 @@ describe Banzai::Filter::ExternalIssueReferenceFilter, lib: true do
     let(:issue) { ExternalIssue.new("#123", project) }
     let(:reference) { issue.to_reference }
 
+    before do
+      project.issues_enabled = false
+      project.save!
+    end
+
     it_behaves_like "external issue tracker"
   end
 
diff --git a/spec/lib/banzai/pipeline/gfm_pipeline_spec.rb b/spec/lib/banzai/pipeline/gfm_pipeline_spec.rb
index 1eb90dc1847..601ffbb5456 100644
--- a/spec/lib/banzai/pipeline/gfm_pipeline_spec.rb
+++ b/spec/lib/banzai/pipeline/gfm_pipeline_spec.rb
@@ -4,26 +4,87 @@ describe Banzai::Pipeline::GfmPipeline do
   describe 'integration between parsing regular and external issue references' do
     let(:project) { create(:redmine_project, :public) }
 
-    it 'allows to use shorthand external reference syntax for Redmine' do
-      markdown = '#12'
+    context 'when internal issue tracker is enabled' do
+      context 'when shorthand pattern #ISSUE_ID is used' do
+        it 'links an internal issue  if it exists' do
+          issue = create(:issue, project: project)
+          markdown = issue.to_reference(project, full: true)
 
-      result = described_class.call(markdown, project: project)[:output]
-      link = result.css('a').first
+          result = described_class.call(markdown, project: project)[:output]
+          link = result.css('a').first
 
-      expect(link['href']).to eq 'http://redmine/projects/project_name_in_redmine/issues/12'
+          expect(link['href']).to eq(
+            Gitlab::Routing.url_helpers.project_issue_path(project, issue)
+          )
+        end
+
+        it 'does not link any issue if it does not exist on GitLab' do
+          markdown = '#12'
+
+          result = described_class.call(markdown, project: project)[:output]
+          expect(result.css('a')).to be_empty
+        end
+      end
+
+      it 'allows to use long external reference syntax for Redmine' do
+        markdown = 'API_32-12'
+
+        result = described_class.call(markdown, project: project)[:output]
+        link = result.css('a').first
+
+        expect(link['href']).to eq 'http://redmine/projects/project_name_in_redmine/issues/12'
+      end
+
+      it 'parses cross-project references to regular issues' do
+        other_project = create(:empty_project, :public)
+        issue = create(:issue, project: other_project)
+        markdown = issue.to_reference(project, full: true)
+
+        result = described_class.call(markdown, project: project)[:output]
+        link = result.css('a').first
+
+        expect(link['href']).to eq(
+          Gitlab::Routing.url_helpers.project_issue_path(other_project, issue)
+        )
+      end
     end
 
-    it 'parses cross-project references to regular issues' do
-      other_project = create(:empty_project, :public)
-      issue = create(:issue, project: other_project)
-      markdown = issue.to_reference(project, full: true)
+    context 'when internal issue tracker is disabled' do
+      before do
+        project.issues_enabled = false
+        project.save!
+      end
 
-      result = described_class.call(markdown, project: project)[:output]
-      link = result.css('a').first
+      it 'allows to use shorthand external reference syntax for Redmine' do
+        markdown = '#12'
 
-      expect(link['href']).to eq(
-        Gitlab::Routing.url_helpers.project_issue_path(other_project, issue)
-      )
+        result = described_class.call(markdown, project: project)[:output]
+        link = result.css('a').first
+
+        expect(link['href']).to eq 'http://redmine/projects/project_name_in_redmine/issues/12'
+      end
+
+      it 'allows to use long external reference syntax for Redmine' do
+        markdown = 'API_32-12'
+
+        result = described_class.call(markdown, project: project)[:output]
+        link = result.css('a').first
+
+        expect(link['href']).to eq 'http://redmine/projects/project_name_in_redmine/issues/12'
+      end
+
+      it 'parses cross-project references to regular issues' do
+        other_project = create(:empty_project, :public)
+        issue = create(:issue, project: other_project)
+        markdown = issue.to_reference(project, full: true)
+
+        result = described_class.call(markdown, project: project)[:output]
+        link = result.css('a').first
+
+        expect(link['href']).to eq(
+          Gitlab::Routing.url_helpers.project_issue_path(other_project, issue)
+        )
+      end
     end
   end
 end
diff --git a/spec/lib/gitlab/reference_extractor_spec.rb b/spec/lib/gitlab/reference_extractor_spec.rb
index 84cfd934fa0..917692e9c6c 100644
--- a/spec/lib/gitlab/reference_extractor_spec.rb
+++ b/spec/lib/gitlab/reference_extractor_spec.rb
@@ -183,11 +183,34 @@ describe Gitlab::ReferenceExtractor, lib: true do
 
   context 'with an external issue tracker' do
     let(:project) { create(:jira_project) }
+    let(:issue)   { create(:issue, project: project) }
 
-    it 'returns JIRA issues for a JIRA-integrated project' do
-      subject.analyze('JIRA-123 and FOOBAR-4567')
-      expect(subject.issues).to eq [ExternalIssue.new('JIRA-123', project),
-                                    ExternalIssue.new('FOOBAR-4567', project)]
+    context 'when GitLab issues are enabled' do
+      it 'returns both JIRA and internal issues' do
+        subject.analyze("JIRA-123 and FOOBAR-4567 and #{issue.to_reference}")
+        expect(subject.issues).to eq [ExternalIssue.new('JIRA-123', project),
+                                      ExternalIssue.new('FOOBAR-4567', project),
+                                      issue]
+      end
+
+      it 'returns only JIRA issues if the internal one does not exists' do
+        subject.analyze("JIRA-123 and FOOBAR-4567 and #999")
+        expect(subject.issues).to eq [ExternalIssue.new('JIRA-123', project),
+                                      ExternalIssue.new('FOOBAR-4567', project)]
+      end
+    end
+
+    context 'when GitLab issues are disabled' do
+      before do
+        project.issues_enabled = false
+        project.save!
+      end
+
+      it 'returns only JIRA issues' do
+        subject.analyze("JIRA-123 and FOOBAR-4567 and #{issue.to_reference}")
+        expect(subject.issues).to eq [ExternalIssue.new('JIRA-123', project),
+                                      ExternalIssue.new('FOOBAR-4567', project)]
+      end
     end
   end
 
diff --git a/spec/models/concerns/mentionable_spec.rb b/spec/models/concerns/mentionable_spec.rb
index e2a29e0ae70..1ad811736af 100644
--- a/spec/models/concerns/mentionable_spec.rb
+++ b/spec/models/concerns/mentionable_spec.rb
@@ -174,25 +174,25 @@ describe Commit, 'Mentionable' do
     it "is false when message doesn't reference anything" do
       allow(commit.raw).to receive(:message).and_return "WIP: Do something"
 
-      expect(commit.matches_cross_reference_regex?).to be false
+      expect(commit.matches_cross_reference_regex?).to be_falsey
     end
 
     it 'is true if issue #number mentioned in title' do
       allow(commit.raw).to receive(:message).and_return "#1"
 
-      expect(commit.matches_cross_reference_regex?).to be true
+      expect(commit.matches_cross_reference_regex?).to be_truthy
     end
 
     it 'is true if references an MR' do
       allow(commit.raw).to receive(:message).and_return "See merge request !12"
 
-      expect(commit.matches_cross_reference_regex?).to be true
+      expect(commit.matches_cross_reference_regex?).to be_truthy
     end
 
     it 'is true if references a commit' do
       allow(commit.raw).to receive(:message).and_return "a1b2c3d4"
 
-      expect(commit.matches_cross_reference_regex?).to be true
+      expect(commit.matches_cross_reference_regex?).to be_truthy
     end
 
     it 'is true if issue referenced by url' do
@@ -200,7 +200,7 @@ describe Commit, 'Mentionable' do
 
       allow(commit.raw).to receive(:message).and_return Gitlab::UrlBuilder.build(issue)
 
-      expect(commit.matches_cross_reference_regex?).to be true
+      expect(commit.matches_cross_reference_regex?).to be_truthy
     end
 
     context 'with external issue tracker' do
@@ -209,7 +209,13 @@ describe Commit, 'Mentionable' do
       it 'is true if external issues referenced' do
         allow(commit.raw).to receive(:message).and_return 'JIRA-123'
 
-        expect(commit.matches_cross_reference_regex?).to be true
+        expect(commit.matches_cross_reference_regex?).to be_truthy
+      end
+
+      it 'is true if internal issues referenced' do
+        allow(commit.raw).to receive(:message).and_return '#123'
+
+        expect(commit.matches_cross_reference_regex?).to be_truthy
       end
     end
   end
diff --git a/spec/models/merge_request_spec.rb b/spec/models/merge_request_spec.rb
index 1eadc28869f..6f6a8ac91b8 100644
--- a/spec/models/merge_request_spec.rb
+++ b/spec/models/merge_request_spec.rb
@@ -155,13 +155,53 @@ describe MergeRequest, models: true do
       expect { subject.cache_merge_request_closes_issues!(subject.author) }.to change(subject.merge_requests_closing_issues, :count).by(1)
     end
 
-    it 'does not cache issues from external trackers' do
-      subject.project.update_attribute(:has_external_issue_tracker, true)
-      issue  = ExternalIssue.new('JIRA-123', subject.project)
-      commit = double('commit1', safe_message: "Fixes #{issue.to_reference}")
-      allow(subject).to receive(:commits).and_return([commit])
+    context 'when both internal and external issue trackers are enabled' do
+      before do
+        subject.project.has_external_issue_tracker = true
+        subject.project.save!
+      end
 
-      expect { subject.cache_merge_request_closes_issues!(subject.author) }.not_to change(subject.merge_requests_closing_issues, :count)
+      it 'does not cache issues from external trackers' do
+        issue  = ExternalIssue.new('JIRA-123', subject.project)
+        commit = double('commit1', safe_message: "Fixes #{issue.to_reference}")
+        allow(subject).to receive(:commits).and_return([commit])
+
+        expect { subject.cache_merge_request_closes_issues!(subject.author) }.not_to change(subject.merge_requests_closing_issues, :count)
+      end
+
+      it 'caches an internal issue' do
+        issue  = create(:issue, project: subject.project)
+        commit = double('commit1', safe_message: "Fixes #{issue.to_reference}")
+        allow(subject).to receive(:commits).and_return([commit])
+
+        expect { subject.cache_merge_request_closes_issues!(subject.author) }
+          .to change(subject.merge_requests_closing_issues, :count).by(1)
+      end
+    end
+
+    context 'when only external issue tracker enabled' do
+      before do
+        subject.project.has_external_issue_tracker = true
+        subject.project.issues_enabled = false
+        subject.project.save!
+      end
+
+      it 'does not cache issues from external trackers' do
+        issue  = ExternalIssue.new('JIRA-123', subject.project)
+        commit = double('commit1', safe_message: "Fixes #{issue.to_reference}")
+        allow(subject).to receive(:commits).and_return([commit])
+
+        expect { subject.cache_merge_request_closes_issues!(subject.author) }.not_to change(subject.merge_requests_closing_issues, :count)
+      end
+
+      it 'does not cache an internal issue' do
+        issue  = create(:issue, project: subject.project)
+        commit = double('commit1', safe_message: "Fixes #{issue.to_reference}")
+        allow(subject).to receive(:commits).and_return([commit])
+
+        expect { subject.cache_merge_request_closes_issues!(subject.author) }
+          .not_to change(subject.merge_requests_closing_issues, :count)
+      end
     end
   end
 
diff --git a/spec/models/project_spec.rb b/spec/models/project_spec.rb
index fdcb011d685..8d916b79b13 100644
--- a/spec/models/project_spec.rb
+++ b/spec/models/project_spec.rb
@@ -533,15 +533,48 @@ describe Project, models: true do
     end
 
     context 'with external issues tracker' do
+      let!(:internal_issue) { create(:issue, project: project) }
       before do
-        allow(project).to receive(:default_issues_tracker?).and_return(false)
+        allow(project).to receive(:external_issue_tracker).and_return(true)
       end
 
-      it 'returns an ExternalIssue' do
-        issue = project.get_issue('FOO-1234', user)
-        expect(issue).to be_kind_of(ExternalIssue)
-        expect(issue.iid).to eq 'FOO-1234'
-        expect(issue.project).to eq project
+      context 'when internal issues are enabled' do
+        it 'returns interlan issue' do
+          issue = project.get_issue(internal_issue.iid, user)
+
+          expect(issue).to be_kind_of(Issue)
+          expect(issue.iid).to eq(internal_issue.iid)
+          expect(issue.project).to eq(project)
+        end
+
+        it 'returns an ExternalIssue when internal issue does not exists' do
+          issue = project.get_issue('FOO-1234', user)
+
+          expect(issue).to be_kind_of(ExternalIssue)
+          expect(issue.iid).to eq('FOO-1234')
+          expect(issue.project).to eq(project)
+        end
+      end
+
+      context 'when internal issues are disabled' do
+        before do
+          project.issues_enabled = false
+          project.save!
+        end
+
+        it 'returns always an External issues' do
+          issue = project.get_issue(internal_issue.iid, user)
+          expect(issue).to be_kind_of(ExternalIssue)
+          expect(issue.iid).to eq(internal_issue.iid.to_s)
+          expect(issue.project).to eq(project)
+        end
+
+        it 'returns an ExternalIssue when internal issue does not exists' do
+          issue = project.get_issue('FOO-1234', user)
+          expect(issue).to be_kind_of(ExternalIssue)
+          expect(issue.iid).to eq('FOO-1234')
+          expect(issue.project).to eq(project)
+        end
       end
     end
   end
diff --git a/spec/policies/project_policy_spec.rb b/spec/policies/project_policy_spec.rb
index ca435dd0218..4ed788af811 100644
--- a/spec/policies/project_policy_spec.rb
+++ b/spec/policies/project_policy_spec.rb
@@ -103,6 +103,30 @@ describe ProjectPolicy, models: true do
     end
   end
 
+  context 'issues feature' do
+    subject { described_class.new(owner, project) }
+
+    context 'when the feature is disabled' do
+      it 'does not include the issues permissions' do
+        project.issues_enabled = false
+        project.save!
+
+        expect_disallowed :read_issue, :create_issue, :update_issue, :admin_issue
+      end
+    end
+
+    context 'when the feature is disabled and external tracker configured' do
+      it 'does not include the issues permissions' do
+        create(:jira_service, project: project)
+
+        project.issues_enabled = false
+        project.save!
+
+        expect_disallowed :read_issue, :create_issue, :update_issue, :admin_issue
+      end
+    end
+  end
+
   context 'abilities for non-public projects' do
     let(:project) { create(:empty_project, namespace: owner.namespace) }
 
diff --git a/spec/requests/api/merge_requests_spec.rb b/spec/requests/api/merge_requests_spec.rb
index 9098ae6bcda..35b6522ea98 100644
--- a/spec/requests/api/merge_requests_spec.rb
+++ b/spec/requests/api/merge_requests_spec.rb
@@ -794,18 +794,24 @@ describe API::MergeRequests do
 
     it 'handles external issues' do
       jira_project = create(:jira_project, :public, name: 'JIR_EXT1')
-      issue = ExternalIssue.new("#{jira_project.name}-123", jira_project)
-      merge_request = create(:merge_request, :simple, author: user, assignee: user, source_project: jira_project)
-      merge_request.update_attribute(:description, "Closes #{issue.to_reference(jira_project)}")
+      ext_issue = ExternalIssue.new("#{jira_project.name}-123", jira_project)
+      issue = create(:issue, project: jira_project)
+      description = "Closes #{ext_issue.to_reference(jira_project)}\ncloses #{issue.to_reference}"
+      merge_request = create(:merge_request,
+        :simple, author: user, assignee: user, source_project: jira_project, description: description)
 
       get api("/projects/#{jira_project.id}/merge_requests/#{merge_request.iid}/closes_issues", user)
 
       expect(response).to have_http_status(200)
       expect(response).to include_pagination_headers
       expect(json_response).to be_an Array
-      expect(json_response.length).to eq(1)
+      expect(json_response.length).to eq(2)
+      expect(json_response.second['title']).to eq(ext_issue.title)
+      expect(json_response.second['id']).to eq(ext_issue.id)
+      expect(json_response.second['confidential']).to be_nil
       expect(json_response.first['title']).to eq(issue.title)
       expect(json_response.first['id']).to eq(issue.id)
+      expect(json_response.first['confidential']).not_to be_nil
     end
 
     it 'returns 403 if the user has no access to the merge request' do
diff --git a/spec/requests/api/projects_spec.rb b/spec/requests/api/projects_spec.rb
index 6dbde8bad31..457f64cc88c 100644
--- a/spec/requests/api/projects_spec.rb
+++ b/spec/requests/api/projects_spec.rb
@@ -159,6 +159,31 @@ describe API::Projects do
         expect(json_response.first).to include 'statistics'
       end
 
+      context 'when external issue tracker is enabled' do
+        let!(:jira_service) { create(:jira_service, project: project) }
+
+        it 'includes open_issues_count' do
+          get api('/projects', user)
+
+          expect(response.status).to eq 200
+          expect(response).to include_pagination_headers
+          expect(json_response).to be_an Array
+          expect(json_response.first.keys).to include('open_issues_count')
+          expect(json_response.find { |hash| hash['id'] == project.id }.keys).to include('open_issues_count')
+        end
+
+        it 'does not include open_issues_count if issues are disabled' do
+          project.project_feature.update_attribute(:issues_access_level, ProjectFeature::DISABLED)
+
+          get api('/projects', user)
+
+          expect(response.status).to eq 200
+          expect(response).to include_pagination_headers
+          expect(json_response).to be_an Array
+          expect(json_response.find { |hash| hash['id'] == project.id }.keys).not_to include('open_issues_count')
+        end
+      end
+
       context 'and with simple=true' do
         it 'returns a simplified version of all the projects' do
           expected_keys = %w(id http_url_to_repo web_url name name_with_namespace path path_with_namespace)
diff --git a/spec/services/git_push_service_spec.rb b/spec/services/git_push_service_spec.rb
index c493c08a7ae..f801506f1b6 100644
--- a/spec/services/git_push_service_spec.rb
+++ b/spec/services/git_push_service_spec.rb
@@ -488,21 +488,57 @@ describe GitPushService, services: true do
           end
         end
 
-        context "using wrong markdown" do
-          let(:message) { "this is some work.\n\ncloses #1" }
+        context "using internal issue reference" do
+          context 'when internal issues are disabled' do
+            before do
+              project.issues_enabled = false
+              project.save!
+            end
+            let(:message) { "this is some work.\n\ncloses #1" }
 
-          it "does not initiates one api call to jira server to close the issue" do
-            execute_service(project, commit_author, @oldrev, @newrev, @ref )
+            it "does not initiates one api call to jira server to close the issue" do
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
 
-            expect(WebMock).not_to have_requested(:post, jira_api_transition_url('JIRA-1'))
+              expect(WebMock).not_to have_requested(:post, jira_api_transition_url('JIRA-1'))
+            end
+
+            it "does not initiates one api call to jira server to comment on the issue" do
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
+
+              expect(WebMock).not_to have_requested(:post, jira_api_comment_url('JIRA-1')).with(
+                body: comment_body
+              ).once
+            end
           end
 
-          it "does not initiates one api call to jira server to comment on the issue" do
-            execute_service(project, commit_author, @oldrev, @newrev, @ref )
+          context 'when internal issues are enabled' do
+            let(:issue) { create(:issue, project: project) }
+            let(:message) { "this is some work.\n\ncloses JIRA-1 \n\n closes #{issue.to_reference}" }
 
-            expect(WebMock).not_to have_requested(:post, jira_api_comment_url('JIRA-1')).with(
-              body: comment_body
-            ).once
+            it "initiates one api call to jira server to close the jira issue" do
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
+
+              expect(WebMock).to have_requested(:post, jira_api_transition_url('JIRA-1')).once
+            end
+
+            it "initiates one api call to jira server to comment on the jira issue" do
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
+
+              expect(WebMock).to have_requested(:post, jira_api_comment_url('JIRA-1')).with(
+                body: comment_body
+              ).once
+            end
+
+            it "closes the internal issue" do
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
+              expect(issue.reload).to be_closed
+            end
+
+            it "adds a note indicating that the issue is now closed" do
+              expect(SystemNoteService).to receive(:change_status)
+                .with(issue, project, commit_author, "closed", closing_commit)
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
+            end
           end
         end
       end
diff --git a/spec/services/issues/close_service_spec.rb b/spec/services/issues/close_service_spec.rb
index d6f4c694069..da8b60f1337 100644
--- a/spec/services/issues/close_service_spec.rb
+++ b/spec/services/issues/close_service_spec.rb
@@ -98,13 +98,13 @@ describe Issues::CloseService, services: true do
       end
     end
 
-    context 'external issue tracker' do
+    context 'internal issues disabled' do
       before do
-        allow(project).to receive(:default_issues_tracker?).and_return(false)
-        described_class.new(project, user).close_issue(issue)
+        project.issues_enabled = false
+        project.save!
       end
 
-      it 'closes the issue' do
+      it 'does not close the issue' do
         expect(issue).to be_valid
         expect(issue).to be_opened
         expect(todo.reload).to be_pending
diff --git a/spec/services/merge_requests/build_service_spec.rb b/spec/services/merge_requests/build_service_spec.rb
index 01ef52396d7..a40d4c877bc 100644
--- a/spec/services/merge_requests/build_service_spec.rb
+++ b/spec/services/merge_requests/build_service_spec.rb
@@ -207,7 +207,7 @@ describe MergeRequests::BuildService, services: true do
         let(:source_branch) { '12345-fix-issue' }
 
         before do
-          allow(project).to receive(:default_issues_tracker?).and_return(false)
+          allow(project).to receive(:external_issue_tracker).and_return(true)
         end
 
         it 'sets the title to: Resolves External Issue $issue-iid' do