diff --git a/app/workers/process_commit_worker.rb b/app/workers/process_commit_worker.rb
index 5b25d980bdbbc2da417d1e645f95564700be30c1..201e7f332b4c39c90788c1e4808c3b816a19c6db 100644
--- a/app/workers/process_commit_worker.rb
+++ b/app/workers/process_commit_worker.rb
@@ -30,10 +30,9 @@ class ProcessCommitWorker
   end
 
   def process_commit_message(project, commit, user, author, default = false)
-    # this is a GitLab generated commit message, ignore it.
-    return if commit.merged_merge_request?(user)
-
-    closed_issues = default ? commit.closes_issues(user) : []
+    # Ignore closing references from GitLab-generated commit messages.
+    find_closing_issues = default && !commit.merged_merge_request?(user)
+    closed_issues = find_closing_issues ? commit.closes_issues(user) : []
 
     close_issues(project, user, author, commit, closed_issues) if closed_issues.any?
     commit.create_cross_references!(author, closed_issues)
diff --git a/spec/workers/process_commit_worker_spec.rb b/spec/workers/process_commit_worker_spec.rb
index 76ef57b6b1e5bfcbc600e2bf8b567880c1b3fa6c..ac79d9c0ac12c78c9e73ced2fd058ac5f80c8529 100644
--- a/spec/workers/process_commit_worker_spec.rb
+++ b/spec/workers/process_commit_worker_spec.rb
@@ -20,32 +20,6 @@ describe ProcessCommitWorker do
       worker.perform(project.id, -1, commit.to_hash)
     end
 
-    context 'when commit is a merge request merge commit' do
-      let(:merge_request) do
-        create(:merge_request,
-               description: "Closes #{issue.to_reference}",
-               source_branch: 'feature-merged',
-               target_branch: 'master',
-               source_project: project)
-      end
-
-      let(:commit) do
-        project.repository.create_branch('feature-merged', 'feature')
-
-        sha = project.repository.merge(user,
-                                       merge_request.diff_head_sha,
-                                       merge_request,
-                                       "Closes #{issue.to_reference}")
-        project.repository.commit(sha)
-      end
-
-      it 'it does not close any issues from the commit message' do
-        expect(worker).not_to receive(:close_issues)
-
-        worker.perform(project.id, user.id, commit.to_hash)
-      end
-    end
-
     it 'processes the commit message' do
       expect(worker).to receive(:process_commit_message).and_call_original
 
@@ -73,13 +47,21 @@ describe ProcessCommitWorker do
 
   describe '#process_commit_message' do
     context 'when pushing to the default branch' do
-      it 'closes issues that should be closed per the commit message' do
+      before do
         allow(commit).to receive(:safe_message).and_return("Closes #{issue.to_reference}")
+      end
 
+      it 'closes issues that should be closed per the commit message' do
         expect(worker).to receive(:close_issues).with(project, user, user, commit, [issue])
 
         worker.process_commit_message(project, commit, user, user, true)
       end
+
+      it 'creates cross references' do
+        expect(commit).to receive(:create_cross_references!).with(user, [issue])
+
+        worker.process_commit_message(project, commit, user, user, true)
+      end
     end
 
     context 'when pushing to a non-default branch' do
@@ -90,12 +72,44 @@ describe ProcessCommitWorker do
 
         worker.process_commit_message(project, commit, user, user, false)
       end
+
+      it 'does not create cross references' do
+        expect(commit).to receive(:create_cross_references!).with(user, [])
+
+        worker.process_commit_message(project, commit, user, user, false)
+      end
     end
 
-    it 'creates cross references' do
-      expect(commit).to receive(:create_cross_references!)
+    context 'when commit is a merge request merge commit to the default branch' do
+      let(:merge_request) do
+        create(:merge_request,
+               description: "Closes #{issue.to_reference}",
+               source_branch: 'feature-merged',
+               target_branch: 'master',
+               source_project: project)
+      end
 
-      worker.process_commit_message(project, commit, user, user)
+      let(:commit) do
+        project.repository.create_branch('feature-merged', 'feature')
+
+        MergeRequests::MergeService
+          .new(project, merge_request.author)
+          .execute(merge_request)
+
+        merge_request.reload.merge_commit
+      end
+
+      it 'does not close any issues from the commit message' do
+        expect(worker).not_to receive(:close_issues)
+
+        worker.process_commit_message(project, commit, user, user, true)
+      end
+
+      it 'still creates cross references' do
+        expect(commit).to receive(:create_cross_references!).with(user, [])
+
+        worker.process_commit_message(project, commit, user, user, true)
+      end
     end
   end