diff --git a/db/post_migrate/20251110012104_prepare_indexes_for_merge_requests_bigint_conversion_stage_two.rb b/db/post_migrate/20251110012104_prepare_indexes_for_merge_requests_bigint_conversion_stage_two.rb
new file mode 100644
index 0000000000000000000000000000000000000000..b2f21341dff5bd65ab14d2ce7f56dce34e8d2bb3
--- /dev/null
+++ b/db/post_migrate/20251110012104_prepare_indexes_for_merge_requests_bigint_conversion_stage_two.rb
@@ -0,0 +1,108 @@
+# frozen_string_literal: true
+
+class PrepareIndexesForMergeRequestsBigintConversionStageTwo < Gitlab::Database::Migration[2.3]
+  include Gitlab::Database::MigrationHelpers::ConvertToBigint
+
+  disable_ddl_transaction!
+  milestone '18.6'
+
+  TABLE_NAME = 'merge_requests'
+  BIGINT_COLUMNS = [
+    :target_project_id_convert_to_bigint,
+    :latest_merge_request_diff_id_convert_to_bigint,
+    :last_edited_by_id_convert_to_bigint
+  ].freeze
+  INDEXES = [
+    {
+      name: 'index_merge_requests_on_target_project_id_and_iid',
+      columns: [:target_project_id_convert_to_bigint, :iid],
+      options: { unique: true }
+    },
+    {
+      name: 'index_merge_requests_on_target_project_id_and_merged_commit_sha',
+      columns: [:target_project_id_convert_to_bigint, :merged_commit_sha]
+    },
+    {
+      name: 'index_merge_requests_on_target_project_id_and_source_branch',
+      columns: [:target_project_id_convert_to_bigint, :source_branch]
+    },
+    {
+      name: 'index_merge_requests_on_target_project_id_and_squash_commit_sha',
+      columns: [:target_project_id_convert_to_bigint, :squash_commit_sha]
+    },
+    {
+      name: 'index_merge_requests_on_target_project_id_and_target_branch',
+      columns: [:target_project_id_convert_to_bigint, :target_branch],
+      options: { where: "state_id = 1 AND merge_when_pipeline_succeeds = true" }
+    },
+    {
+      name: 'index_merge_requests_for_latest_diffs_with_state_merged',
+      columns: [:latest_merge_request_diff_id_convert_to_bigint, :target_project_id_convert_to_bigint],
+      options: { where: "state_id = 3" }
+    },
+    {
+      name: 'index_merge_requests_on_latest_merge_request_diff_id',
+      columns: [:latest_merge_request_diff_id_convert_to_bigint]
+    },
+    {
+      name: 'idx_mrs_on_target_id_and_created_at_and_state_id',
+      columns: [:target_project_id_convert_to_bigint, :state_id, :created_at, :id]
+    },
+    {
+      name: 'index_merge_requests_on_target_project_id_and_created_at_and_id',
+      columns: [:target_project_id_convert_to_bigint, :created_at, :id]
+    },
+    {
+      name: 'index_merge_requests_on_target_project_id_and_updated_at_and_id',
+      columns: [:target_project_id_convert_to_bigint, :updated_at, :id]
+    },
+    {
+      name: 'index_merge_requests_on_tp_id_and_merge_commit_sha_and_id',
+      columns: [:target_project_id_convert_to_bigint, :merge_commit_sha, :id]
+    },
+    {
+      name: 'index_merge_requests_on_author_id_and_target_project_id',
+      columns: [:author_id, :target_project_id_convert_to_bigint]
+    },
+    {
+      name: 'index_on_merge_requests_for_latest_diffs',
+      columns: [:target_project_id_convert_to_bigint],
+      options: { include: [:id, :latest_merge_request_diff_id_convert_to_bigint] }
+    }
+  ].freeze
+
+  def up
+    return if skip_migration?
+
+    # rubocop:disable Migration/PreventIndexCreation -- Bigint migration
+    INDEXES.each do |index|
+      options = index[:options] || {}
+      prepare_async_index(TABLE_NAME, index[:columns], name: bigint_index_name(index[:name]), **options)
+    end
+    # rubocop:enable Migration/PreventIndexCreation
+  end
+
+  def down
+    return if skip_migration?
+
+    INDEXES.each do |index|
+      options = index[:options] || {}
+      unprepare_async_index(TABLE_NAME, index[:columns], name: bigint_index_name(index[:name]), **options)
+    end
+  end
+
+  private
+
+  def skip_migration?
+    unless conversion_columns_exist?
+      say "No conversion columns found - migration skipped"
+      return true
+    end
+
+    false
+  end
+
+  def conversion_columns_exist?
+    BIGINT_COLUMNS.all? { |column| column_exists?(TABLE_NAME, column) }
+  end
+end
diff --git a/db/schema_migrations/20251110012104 b/db/schema_migrations/20251110012104
new file mode 100644
index 0000000000000000000000000000000000000000..a7c40317933bab4feebb52cac81dd51aa66fe7bd
--- /dev/null
+++ b/db/schema_migrations/20251110012104
@@ -0,0 +1 @@
+7070de0ba07af23a7c45a9709d5941d426b0e2724eed2da617398af9fae2a1a9
\ No newline at end of file