diff --git a/db/docs/batched_background_migrations/backfill_project_id_on_merge_request_diff_files.yml b/db/docs/batched_background_migrations/backfill_project_id_on_merge_request_diff_files.yml
new file mode 100644
index 0000000000000000000000000000000000000000..6429acd4c4e6da76b93b0f2b012eef35eb2a932e
--- /dev/null
+++ b/db/docs/batched_background_migrations/backfill_project_id_on_merge_request_diff_files.yml
@@ -0,0 +1,8 @@
+---
+migration_job_name: BackfillProjectIdOnMergeRequestDiffFiles
+description: Backfills nil project_ids on merge_request_diff_files
+feature_category: source_code_management
+introduced_by_url: https://gitlab.com/gitlab-org/gitlab/-/merge_requests/123123123123
+milestone: '18.3'
+queued_migration_version: 20250717193053
+finalized_by: # version of the migration that finalized this BBM
diff --git a/db/post_migrate/20250717193053_queue_backfill_project_id_on_merge_request_diff_files.rb b/db/post_migrate/20250717193053_queue_backfill_project_id_on_merge_request_diff_files.rb
new file mode 100644
index 0000000000000000000000000000000000000000..12640ab7645f4ed00d056cc1af609ababc044a76
--- /dev/null
+++ b/db/post_migrate/20250717193053_queue_backfill_project_id_on_merge_request_diff_files.rb
@@ -0,0 +1,27 @@
+# frozen_string_literal: true
+
+class QueueBackfillProjectIdOnMergeRequestDiffFiles < Gitlab::Database::Migration[2.3]
+  milestone '18.3'
+
+  restrict_gitlab_migration gitlab_schema: :gitlab_main
+
+  MIGRATION = "BackfillProjectIdOnMergeRequestDiffFiles"
+  DELAY_INTERVAL = 2.minutes
+  BATCH_SIZE = 1000
+  SUB_BATCH_SIZE = 100
+
+  def up
+    queue_batched_background_migration(
+      MIGRATION,
+      :merge_request_diff_files,
+      :project_id,
+      job_interval: DELAY_INTERVAL,
+      batch_size: BATCH_SIZE,
+      sub_batch_size: SUB_BATCH_SIZE
+    )
+  end
+
+  def down
+    delete_batched_background_migration(MIGRATION, :merge_request_diff_files, :project_id, [])
+  end
+end
diff --git a/db/schema_migrations/20250717193053 b/db/schema_migrations/20250717193053
new file mode 100644
index 0000000000000000000000000000000000000000..0b593a4378a447836bc33ba94b9dc6828759eb25
--- /dev/null
+++ b/db/schema_migrations/20250717193053
@@ -0,0 +1 @@
+2caddcd00637f8b18382524ddd31016f2c0e7c58224e232b7536e99610575213
\ No newline at end of file
diff --git a/lib/gitlab/background_migration/backfill_project_id_on_merge_request_diff_files.rb b/lib/gitlab/background_migration/backfill_project_id_on_merge_request_diff_files.rb
new file mode 100644
index 0000000000000000000000000000000000000000..57388d749a1c2d5ac971c2a29502d6b861e69254
--- /dev/null
+++ b/lib/gitlab/background_migration/backfill_project_id_on_merge_request_diff_files.rb
@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+# See https://docs.gitlab.com/ee/development/database/batched_background_migrations.html
+# for more information on how to use batched background migrations
+
+# Update below commented lines with appropriate values.
+
+module Gitlab
+  module BackgroundMigration
+    class BackfillProjectIdOnMergeRequestDiffFiles < BatchedMigrationJob
+      feature_category :source_code_management
+
+      operation_name :backfill_project_id_on_merge_request_diff_files
+      scope_to ->(relation) { relation.where(project_id: nil) } # rubocop: disable Database/AvoidScopeTo -- `project_id` is an indexed column
+
+      def construct_query(sub_batch:)
+        <<~SQL
+            UPDATE merge_request_diff_files
+            SET project_id = merge_request_diffs.project_id
+            FROM merge_request_diffs
+            WHERE merge_request_diffs.id = merge_request_diff_files.merge_request_diff_id
+              AND merge_request_diff_files.id IN (#{sub_batch.select(:id).to_sql})
+        SQL
+      end
+
+      def perform
+        each_sub_batch do |sub_batch|
+          connection.execute(construct_query(sub_batch: sub_batch))
+        end
+      end
+    end
+  end
+end
diff --git a/spec/lib/gitlab/background_migration/backfill_project_id_on_merge_request_diff_files_spec.rb b/spec/lib/gitlab/background_migration/backfill_project_id_on_merge_request_diff_files_spec.rb
new file mode 100644
index 0000000000000000000000000000000000000000..11cfb4ef27222e6a17be877d87799709a1223896
--- /dev/null
+++ b/spec/lib/gitlab/background_migration/backfill_project_id_on_merge_request_diff_files_spec.rb
@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+require 'spec_helper'
+
+RSpec.describe Gitlab::BackgroundMigration::BackfillProjectIdOnMergeRequestDiffFiles, feature_category: :source_code_management do
+  # This is a fake test, obviously, to satisfy rubocop so I can make a checkpoint
+  #   commit.
+  #
+  it "true" do
+    foo = 1
+    expect(foo).to be(true)
+  end
+end
diff --git a/spec/migrations/20250717193053_queue_backfill_project_id_on_merge_request_diff_files_spec.rb b/spec/migrations/20250717193053_queue_backfill_project_id_on_merge_request_diff_files_spec.rb
new file mode 100644
index 0000000000000000000000000000000000000000..ea045822267882ae0ddcfba7b29889654a84d53d
--- /dev/null
+++ b/spec/migrations/20250717193053_queue_backfill_project_id_on_merge_request_diff_files_spec.rb
@@ -0,0 +1,27 @@
+# frozen_string_literal: true
+
+require 'spec_helper'
+require_migration!
+
+RSpec.describe QueueBackfillProjectIdOnMergeRequestDiffFiles, migration: :gitlab_main, feature_category: :source_code_management do
+  let!(:batched_migration) { described_class::MIGRATION }
+
+  it 'schedules a new batched migration' do
+    reversible_migration do |migration|
+      migration.before -> {
+        expect(batched_migration).not_to have_scheduled_batched_migration
+      }
+
+      migration.after -> {
+        expect(batched_migration).to have_scheduled_batched_migration(
+          gitlab_schema: :gitlab_main,
+          table_name: :merge_request_diff_files,
+          column_name: :project_id,
+          interval: described_class::DELAY_INTERVAL,
+          batch_size: described_class::BATCH_SIZE,
+          sub_batch_size: described_class::SUB_BATCH_SIZE
+        )
+      }
+    end
+  end
+end