diff --git a/app/finders/projects_finder.rb b/app/finders/projects_finder.rb
index cac6643eff3..0398ccce93b 100644
--- a/app/finders/projects_finder.rb
+++ b/app/finders/projects_finder.rb
@@ -49,6 +49,7 @@ class ProjectsFinder < UnionFinder
     collection = by_search(collection)
     collection = by_archived(collection)
     collection = by_custom_attributes(collection)
+    collection = by_deleted_status(collection)
 
     sort(collection)
   end
@@ -131,6 +132,10 @@ class ProjectsFinder < UnionFinder
     params[:search].present? ? items.search(params[:search]) : items
   end
 
+  def by_deleted_status(items)
+    params[:without_deleted].present? ? items.without_deleted : items
+  end
+
   def sort(items)
     params[:sort].present? ? items.sort_by_attribute(params[:sort]) : items.order_id_desc
   end
diff --git a/changelogs/unreleased/50678-ignores-project-pending-delete.yml b/changelogs/unreleased/50678-ignores-project-pending-delete.yml
new file mode 100644
index 00000000000..e4594abba99
--- /dev/null
+++ b/changelogs/unreleased/50678-ignores-project-pending-delete.yml
@@ -0,0 +1,5 @@
+---
+title: Excludes project marked from deletion to projects API
+merge_request: 21542
+author: Jacopo Beschi @jacopo-beschi
+type: changed
diff --git a/lib/api/helpers.rb b/lib/api/helpers.rb
index 5505d7a7b08..c7ecddeccf0 100644
--- a/lib/api/helpers.rb
+++ b/lib/api/helpers.rb
@@ -103,10 +103,12 @@ module API
     end
 
     def find_project(id)
+      projects = Project.without_deleted
+
       if id.is_a?(Integer) || id =~ /^\d+$/
-        Project.find_by(id: id)
+        projects.find_by(id: id)
       elsif id.include?("/")
-        Project.find_by_full_path(id)
+        projects.find_by_full_path(id)
       end
     end
 
@@ -386,7 +388,7 @@ module API
     end
 
     def project_finder_params
-      finder_params = {}
+      finder_params = { without_deleted: true }
       finder_params[:owned] = true if params[:owned].present?
       finder_params[:non_public] = true if params[:membership].present?
       finder_params[:starred] = true if params[:starred].present?
diff --git a/spec/finders/projects_finder_spec.rb b/spec/finders/projects_finder_spec.rb
index 7931ad9b9f0..590e838f13e 100644
--- a/spec/finders/projects_finder_spec.rb
+++ b/spec/finders/projects_finder_spec.rb
@@ -174,6 +174,13 @@ describe ProjectsFinder do
       end
     end
 
+    describe 'filter by without_deleted' do
+      let(:params) { { without_deleted: true } }
+      let!(:pending_delete_project) { create(:project, :public, pending_delete: true) }
+
+      it { is_expected.to match_array([public_project, internal_project]) }
+    end
+
     describe 'sorting' do
       let(:params) { { sort: 'name_asc' } }
 
diff --git a/spec/requests/api/projects_spec.rb b/spec/requests/api/projects_spec.rb
index 65cd423f0bb..c8e98e6024c 100644
--- a/spec/requests/api/projects_spec.rb
+++ b/spec/requests/api/projects_spec.rb
@@ -148,6 +148,16 @@ describe API::Projects do
         expect(json_response.first.keys).to include('open_issues_count')
       end
 
+      it 'does not include projects marked for deletion' do
+        project.update(pending_delete: true)
+
+        get api('/projects', user)
+
+        expect(response).to have_gitlab_http_status(200)
+        expect(json_response).to be_an Array
+        expect(json_response.map { |p| p['id'] }).not_to include(project.id)
+      end
+
       it 'does not include open_issues_count if issues are disabled' do
         project.project_feature.update_attribute(:issues_access_level, ProjectFeature::DISABLED)
 
@@ -1012,6 +1022,15 @@ describe API::Projects do
         expect(json_response).not_to include("import_error")
       end
 
+      it 'returns 404 when project is marked for deletion' do
+        project.update(pending_delete: true)
+
+        get api("/projects/#{project.id}", user)
+
+        expect(response).to have_gitlab_http_status(404)
+        expect(json_response['message']).to eq('404 Project Not Found')
+      end
+
       context 'links exposure' do
         it 'exposes related resources full URIs' do
           get api("/projects/#{project.id}", user)