diff --git a/app/controllers/projects/branches_controller.rb b/app/controllers/projects/branches_controller.rb
index df4002d075b..b3dfafb7b87 100644
--- a/app/controllers/projects/branches_controller.rb
+++ b/app/controllers/projects/branches_controller.rb
@@ -64,8 +64,9 @@ class Projects::BranchesController < Projects::ApplicationController
     success = (result[:status] == :success)
 
     if params[:issue_iid] && success
-      issue = IssuesFinder.new(current_user, project_id: (confidential_issue_project || @project).id).find_by(iid: params[:issue_iid])
-      SystemNoteService.new_issue_branch(issue, @project, current_user, branch_name) if issue
+      target_project = confidential_issue_project || @project
+      issue = IssuesFinder.new(current_user, project_id: target_project.id).find_by(iid: params[:issue_iid])
+      SystemNoteService.new_issue_branch(issue, target_project, current_user, branch_name, branch_project: @project) if issue
     end
 
     respond_to do |format|
diff --git a/app/services/merge_requests/create_from_issue_service.rb b/app/services/merge_requests/create_from_issue_service.rb
index 074a45e328b..2a217a6f689 100644
--- a/app/services/merge_requests/create_from_issue_service.rb
+++ b/app/services/merge_requests/create_from_issue_service.rb
@@ -25,11 +25,11 @@ module MergeRequests
       new_merge_request = create(merge_request)
 
       if new_merge_request.valid?
-        SystemNoteService.new_merge_request(issue, target_project, current_user, new_merge_request)
+        SystemNoteService.new_merge_request(issue, project, current_user, new_merge_request)
 
         success(new_merge_request)
       else
-        SystemNoteService.new_issue_branch(issue, target_project, current_user, branch_name)
+        SystemNoteService.new_issue_branch(issue, project, current_user, branch_name, branch_project: target_project)
 
         error(new_merge_request.errors)
       end
diff --git a/app/services/system_note_service.rb b/app/services/system_note_service.rb
index 1390f7cdf46..8f7cfe582ca 100644
--- a/app/services/system_note_service.rb
+++ b/app/services/system_note_service.rb
@@ -404,8 +404,9 @@ module SystemNoteService
   # Example note text:
   #
   #   "created branch `201-issue-branch-button`"
-  def new_issue_branch(issue, project, author, branch)
-    link = url_helpers.project_compare_path(project, from: project.default_branch, to: branch)
+  def new_issue_branch(issue, project, author, branch, branch_project: nil)
+    branch_project ||= project
+    link = url_helpers.project_compare_path(branch_project, from: branch_project.default_branch, to: branch)
 
     body = "created branch [`#{branch}`](#{link}) to address this issue"
 
@@ -413,7 +414,7 @@ module SystemNoteService
   end
 
   def new_merge_request(issue, project, author, merge_request)
-    body = "created merge request #{merge_request.to_reference} to address this issue"
+    body = "created merge request #{merge_request.to_reference(project)} to address this issue"
 
     create_note(NoteSummary.new(issue, project, author, body, action: 'merge'))
   end
diff --git a/spec/controllers/projects/branches_controller_spec.rb b/spec/controllers/projects/branches_controller_spec.rb
index 8c349b1e988..712c3fa0ffe 100644
--- a/spec/controllers/projects/branches_controller_spec.rb
+++ b/spec/controllers/projects/branches_controller_spec.rb
@@ -92,7 +92,7 @@ describe Projects::BranchesController do
       end
 
       it 'posts a system note' do
-        expect(SystemNoteService).to receive(:new_issue_branch).with(issue, project, user, "1-feature-branch")
+        expect(SystemNoteService).to receive(:new_issue_branch).with(issue, project, user, "1-feature-branch", branch_project: project)
 
         post :create,
              params: {
diff --git a/spec/services/merge_requests/create_from_issue_service_spec.rb b/spec/services/merge_requests/create_from_issue_service_spec.rb
index 2c83b2851a1..0e0da6a13ab 100644
--- a/spec/services/merge_requests/create_from_issue_service_spec.rb
+++ b/spec/services/merge_requests/create_from_issue_service_spec.rb
@@ -48,7 +48,7 @@ describe MergeRequests::CreateFromIssueService do
       end
 
       it 'creates the new_merge_request system note' do
-        expect(SystemNoteService).to receive(:new_merge_request).with(issue, target_project, user, instance_of(MergeRequest))
+        expect(SystemNoteService).to receive(:new_merge_request).with(issue, project, user, instance_of(MergeRequest))
 
         service.execute
       end
@@ -56,7 +56,7 @@ describe MergeRequests::CreateFromIssueService do
       it 'creates the new_issue_branch system note when the branch could be created but the merge_request cannot be created' do
         expect_any_instance_of(MergeRequest).to receive(:valid?).at_least(:once).and_return(false)
 
-        expect(SystemNoteService).to receive(:new_issue_branch).with(issue, target_project, user, issue.to_branch_name)
+        expect(SystemNoteService).to receive(:new_issue_branch).with(issue, project, user, issue.to_branch_name, branch_project: target_project)
 
         service.execute
       end
diff --git a/spec/services/system_note_service_spec.rb b/spec/services/system_note_service_spec.rb
index 93fe3290d8b..97377c2f560 100644
--- a/spec/services/system_note_service_spec.rb
+++ b/spec/services/system_note_service_spec.rb
@@ -454,16 +454,32 @@ describe SystemNoteService do
   end
 
   describe '.new_issue_branch' do
-    subject { described_class.new_issue_branch(noteable, project, author, "1-mepmep") }
+    let(:branch) { '1-mepmep' }
 
-    it_behaves_like 'a system note' do
-      let(:action) { 'branch' }
+    subject { described_class.new_issue_branch(noteable, project, author, branch, branch_project: branch_project) }
+
+    shared_examples_for 'a system note for new issue branch' do
+      it_behaves_like 'a system note' do
+        let(:action) { 'branch' }
+      end
+
+      context 'when a branch is created from the new branch button' do
+        it 'sets the note text' do
+          expect(subject.note).to start_with("created branch [`#{branch}`]")
+        end
+      end
     end
 
-    context 'when a branch is created from the new branch button' do
-      it 'sets the note text' do
-        expect(subject.note).to start_with("created branch [`1-mepmep`]")
-      end
+    context 'branch_project is set' do
+      let(:branch_project) { create(:project, :repository) }
+
+      it_behaves_like 'a system note for new issue branch'
+    end
+
+    context 'branch_project is not set' do
+      let(:branch_project) { nil }
+
+      it_behaves_like 'a system note for new issue branch'
     end
   end
 
@@ -477,7 +493,7 @@ describe SystemNoteService do
     end
 
     it 'sets the new merge request note text' do
-      expect(subject.note).to eq("created merge request #{merge_request.to_reference} to address this issue")
+      expect(subject.note).to eq("created merge request #{merge_request.to_reference(project)} to address this issue")
     end
   end