diff --git a/app/services/projects/destroy_service.rb b/app/services/projects/destroy_service.rb
index 12d7ed15d00aef3ab542767d8ef49f8c9fac5c3a..403f7d69bc1346544de0db3f8108fa48d718d198 100644
--- a/app/services/projects/destroy_service.rb
+++ b/app/services/projects/destroy_service.rb
@@ -212,18 +212,44 @@ def log_destroy_event
     def destroy_mr_diff_relations!
       delete_batch_size = 1000
 
-      project.merge_requests.each_batch(column: :iid, of: BATCH_SIZE) do |relation_ids|
-        loop do
-          inner_query = MergeRequestDiffFile
-            .select(:merge_request_diff_id, :relative_order)
-            .where(merge_request_diff_id: MergeRequestDiff.where(merge_request_id: relation_ids).select(:id))
-            .limit(delete_batch_size)
-
-          deleted_rows = MergeRequestDiffFile
-            .where("(merge_request_diff_files.merge_request_diff_id, merge_request_diff_files.relative_order) IN (?)", inner_query)
-            .delete_all
-
-          break if deleted_rows == 0
+      if Feature.enabled?(:merge_request_diff_commits_partition, project)
+        # partition compatible queries
+        project.merge_requests.each_batch(column: :iid, of: BATCH_SIZE) do |relation_ids|
+          loop do
+            inner_query = MergeRequestDiffCommit
+              .select(:merge_request_diff_id, :relative_order)
+              .where(
+                merge_request_diff_id: MergeRequestDiff.where(merge_request_id: relation_ids).select(:id)
+              )
+              .where(project_id: project.id)
+              .limit(delete_batch_size)
+
+            deleted_rows = MergeRequestDiffCommit
+              .where(project_id: project.id)
+              .where(
+                "(merge_request_diff_commits.merge_request_diff_id, merge_request_diff_commits.relative_order) IN (?)",
+                inner_query
+              )
+              .delete_all
+
+            break if deleted_rows == 0
+          end
+        end
+      else
+        # records without project ids
+        project.merge_requests.each_batch(column: :iid, of: BATCH_SIZE) do |relation_ids|
+          loop do
+            inner_query = MergeRequestDiffFile
+              .select(:merge_request_diff_id, :relative_order)
+              .where(merge_request_diff_id: MergeRequestDiff.where(merge_request_id: relation_ids).select(:id))
+              .limit(delete_batch_size)
+
+            deleted_rows = MergeRequestDiffFile
+              .where("(merge_request_diff_files.merge_request_diff_id, merge_request_diff_files.relative_order) IN (?)", inner_query)
+              .delete_all
+
+            break if deleted_rows == 0
+          end
         end
       end
 
diff --git a/spec/services/projects/destroy_service_spec.rb b/spec/services/projects/destroy_service_spec.rb
index 34e78907b559fb7e2833cec6838ae026f95bd645..a4655c5348b465a1c6607beb4a2377b9c10e3aae 100644
--- a/spec/services/projects/destroy_service_spec.rb
+++ b/spec/services/projects/destroy_service_spec.rb
@@ -1087,6 +1087,62 @@
     end
   end
 
+  describe '#destroy_mr_diff_relations!' do
+    let(:service) { described_class.new(project, user, {}) }
+
+    context 'when merge_request_diff_commits_partition feature flag is enabled' do
+      let!(:merge_request) { create(:merge_request, source_project: project) }
+      let!(:merge_request_diff) { merge_request.merge_request_diffs.first }
+
+      before do
+        MergeRequestDiffCommit.where(merge_request_diff_id: merge_request_diff.id).delete_all
+
+        3.times do |i|
+          MergeRequestDiffCommit.create!(
+            merge_request_diff_id: merge_request_diff.id,
+            project_id: project.id,
+            relative_order: i,
+            sha: Digest::SHA256.hexdigest("commit-#{i}"),
+            authored_date: Time.current,
+            committed_date: Time.current
+          )
+        end
+      end
+
+      it 'deletes MergeRequestDiffCommit records using partition-compatible queries' do
+        expect(MergeRequestDiffCommit.where(project_id: project.id).count).to eq(3)
+
+        service.send(:destroy_mr_diff_relations!)
+
+        expect(MergeRequestDiffCommit.where(project_id: project.id).count).to eq(0)
+      end
+
+      it 'only deletes records for the current project' do
+        other_project = create(:project, :repository, namespace: user.namespace)
+        other_merge_request = create(:merge_request, source_project: other_project)
+        other_diff = other_merge_request.merge_request_diffs.first
+
+        MergeRequestDiffCommit.where(merge_request_diff_id: other_diff.id).delete_all
+
+        2.times do |i|
+          MergeRequestDiffCommit.create!(
+            merge_request_diff_id: other_diff.id,
+            project_id: other_project.id,
+            relative_order: i,
+            sha: Digest::SHA256.hexdigest("other-commit-#{i}"),
+            authored_date: Time.current,
+            committed_date: Time.current
+          )
+        end
+
+        service.send(:destroy_mr_diff_relations!)
+
+        expect(MergeRequestDiffCommit.where(project_id: project.id).count).to eq(0)
+        expect(MergeRequestDiffCommit.where(project_id: other_project.id).count).to eq(2)
+      end
+    end
+  end
+
   def destroy_project(project, user, params = {})
     described_class.new(project, user, params).public_send(async ? :async_execute : :execute)
   end