diff --git a/db/docs/batched_background_migrations/backfill_system_note_metadata_namespace_id.yml b/db/docs/batched_background_migrations/backfill_system_note_metadata_namespace_id.yml
new file mode 100644
index 0000000000000000000000000000000000000000..15b9e00efbad920fabc0d6f346fdb779b45589ba
--- /dev/null
+++ b/db/docs/batched_background_migrations/backfill_system_note_metadata_namespace_id.yml
@@ -0,0 +1,8 @@
+---
+migration_job_name: BackfillSystemNoteMetadataNamespaceId
+description: Backfills namespace_id for every system_note_metadata record
+feature_category: team_planning
+introduced_by_url: https://gitlab.com/gitlab-org/gitlab/-/merge_requests/209714
+milestone: '18.6'
+queued_migration_version: 20251021184303
+finalized_by: # version of the migration that finalized this BBM
diff --git a/db/post_migrate/20251021184303_queue_backfill_system_note_metadata_namespace_id.rb b/db/post_migrate/20251021184303_queue_backfill_system_note_metadata_namespace_id.rb
new file mode 100644
index 0000000000000000000000000000000000000000..1b8784003e6630add08364fce3e256886a413dcc
--- /dev/null
+++ b/db/post_migrate/20251021184303_queue_backfill_system_note_metadata_namespace_id.rb
@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+
+class QueueBackfillSystemNoteMetadataNamespaceId < Gitlab::Database::Migration[2.3]
+  milestone '18.6'
+  restrict_gitlab_migration gitlab_schema: :gitlab_main_org
+
+  MIGRATION = "BackfillSystemNoteMetadataNamespaceId"
+  BATCH_SIZE = 30_000
+  SUB_BATCH_SIZE = 250
+
+  def up
+    queue_batched_background_migration(
+      MIGRATION,
+      :system_note_metadata,
+      :id,
+      batch_size: BATCH_SIZE,
+      sub_batch_size: SUB_BATCH_SIZE
+    )
+  end
+
+  def down
+    delete_batched_background_migration(MIGRATION, :system_note_metadata, :id, [])
+  end
+end
diff --git a/db/schema_migrations/20251021184303 b/db/schema_migrations/20251021184303
new file mode 100644
index 0000000000000000000000000000000000000000..0637ce0439794fa105fe03b3a982c60d30426965
--- /dev/null
+++ b/db/schema_migrations/20251021184303
@@ -0,0 +1 @@
+94512c6e7aad948c253d50290a4f3719339b32aeb8ffc999784417f871a57e29
\ No newline at end of file
diff --git a/lib/gitlab/background_migration/backfill_system_note_metadata_namespace_id.rb b/lib/gitlab/background_migration/backfill_system_note_metadata_namespace_id.rb
new file mode 100644
index 0000000000000000000000000000000000000000..2657697c1d6539a0208c6f2577b1f71c770a0c93
--- /dev/null
+++ b/lib/gitlab/background_migration/backfill_system_note_metadata_namespace_id.rb
@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Gitlab
+  module BackgroundMigration
+    class BackfillSystemNoteMetadataNamespaceId < BatchedMigrationJob
+      operation_name :set_namespace_id_on_system_note_metadata_records
+      feature_category :team_planning
+
+      def perform
+        each_sub_batch do |sub_batch|
+          connection.execute(
+            <<~SQL
+              WITH relation AS MATERIALIZED (
+                #{sub_batch.select(:id, :note_id).limit(sub_batch_size).to_sql}
+              ), relation_with_namespace_id AS MATERIALIZED (
+                SELECT "relation".*, COALESCE("projects"."project_namespace_id", "notes"."namespace_id") AS namespace_id
+                FROM "relation" INNER JOIN "notes" ON "notes"."id" = "relation"."note_id"
+                LEFT JOIN "projects" ON "projects"."id" = "notes"."project_id"
+                LIMIT #{sub_batch_size}
+              )
+              UPDATE "system_note_metadata"
+              SET "namespace_id" = "relation_with_namespace_id"."namespace_id"
+              FROM "relation_with_namespace_id"
+              WHERE "system_note_metadata"."id" = "relation_with_namespace_id"."id"
+            SQL
+          )
+        end
+      end
+    end
+  end
+end
diff --git a/spec/lib/gitlab/background_migration/backfill_system_note_metadata_namespace_id_spec.rb b/spec/lib/gitlab/background_migration/backfill_system_note_metadata_namespace_id_spec.rb
new file mode 100644
index 0000000000000000000000000000000000000000..fc1ea46785ac3877b560e25844450a25da8031c2
--- /dev/null
+++ b/spec/lib/gitlab/background_migration/backfill_system_note_metadata_namespace_id_spec.rb
@@ -0,0 +1,180 @@
+# frozen_string_literal: true
+
+require 'spec_helper'
+
+RSpec.describe Gitlab::BackgroundMigration::BackfillSystemNoteMetadataNamespaceId, feature_category: :team_planning do
+  # rubocop:disable RSpec/MultipleMemoizedHelpers -- Necessary for backfill setup
+  let(:namespaces) { table(:namespaces) }
+  let(:notes) { table(:notes) }
+  let(:projects) { table(:projects) }
+  let(:system_note_metadata) { table(:system_note_metadata) }
+  let(:users) { table(:users) }
+  let(:organization) { table(:organizations).create!(name: 'organization', path: 'organization') }
+  let(:project_namespace1) do
+    table(:namespaces).create!(name: 'project1', path: 'project1', organization_id: organization.id)
+  end
+
+  let(:project_namespace2) do
+    table(:namespaces).create!(name: 'project2', path: 'project2', organization_id: organization.id)
+  end
+
+  let(:group_namespace1) do
+    table(:namespaces).create!(name: 'group1', path: 'group1', organization_id: organization.id)
+  end
+
+  let(:group_namespace2) do
+    table(:namespaces).create!(name: 'group2', path: 'group2', organization_id: organization.id)
+  end
+
+  let(:project1) do
+    table(:projects).create!(
+      namespace_id: group_namespace1.id,
+      project_namespace_id: project_namespace1.id,
+      organization_id: organization.id
+    )
+  end
+
+  let(:project2) do
+    table(:projects).create!(
+      namespace_id: group_namespace2.id,
+      project_namespace_id: project_namespace2.id,
+      organization_id: organization.id
+    )
+  end
+
+  let(:user) do
+    users.create!(
+      username: 'john_doe', email: 'johndoe@gitlab.com', projects_limit: 10, organization_id: organization.id
+    )
+  end
+
+  let(:note1) do
+    notes.create!(
+      project_id: project1.id,
+      namespace_id: nil,
+      noteable_type: 'Issue',
+      noteable_id: 1,
+      author_id: user.id
+    )
+  end
+
+  let(:note_metadata1) { system_note_metadata.create!(note_id: note1.id) }
+  let(:note2) do
+    notes.create!(
+      project_id: project2.id,
+      namespace_id: group_namespace2.id, # Wrong namespace so we can test precedence with project_id column
+      noteable_type: 'Issue',
+      noteable_id: 2,
+      author_id: user.id
+    )
+  end
+
+  let(:note_metadata2) { system_note_metadata.create!(note_id: note2.id) }
+  let(:note3) do
+    notes.create!(
+      project_id: nil,
+      namespace_id: group_namespace1.id,
+      noteable_type: 'Issue',
+      noteable_id: 3,
+      author_id: user.id
+    )
+  end
+
+  let(:note_metadata3) { system_note_metadata.create!(note_id: note3.id) }
+  let(:note4) do
+    notes.create!(
+      project_id: nil,
+      namespace_id: group_namespace2.id,
+      noteable_type: 'Issue',
+      noteable_id: 4,
+      author_id: user.id
+    )
+  end
+
+  let(:note_metadata4) { system_note_metadata.create!(note_id: note4.id) }
+  let(:note5) do
+    notes.create!(
+      project_id: project1.id,
+      namespace_id: project_namespace1.id,
+      noteable_type: 'Issue',
+      noteable_id: 5,
+      author_id: user.id
+    )
+  end
+
+  let(:note_metadata5) { system_note_metadata.create!(note_id: note5.id, namespace_id: project_namespace1.id) }
+
+  let(:note6) do
+    notes.create!(
+      project_id: project2.id,
+      namespace_id: group_namespace2.id,
+      noteable_type: 'Issue',
+      noteable_id: 6,
+      author_id: user.id
+    )
+  end
+
+  let(:note_metadata6) { system_note_metadata.create!(note_id: note6.id, namespace_id: group_namespace2.id) }
+
+  describe '#perform' do
+    let(:migration) do
+      start_id, end_id = system_note_metadata.pick('MIN(id), MAX(id)')
+
+      described_class.new(
+        start_id: start_id,
+        end_id: end_id,
+        batch_table: :system_note_metadata,
+        batch_column: :id,
+        sub_batch_size: 2,
+        pause_ms: 0,
+        job_arguments: [],
+        connection: ApplicationRecord.connection
+      )
+    end
+
+    subject(:migrate) { migration.perform }
+
+    before do
+      system_note_metadata.connection.execute(<<~SQL)
+        -- Necessary as the constraint won't allow new invalid records to be created
+        ALTER TABLE system_note_metadata DROP CONSTRAINT check_9135b6f0b6;
+        -- Also disabling the trigger that will set the correct value in the column
+        ALTER TABLE system_note_metadata DISABLE TRIGGER ALL;
+      SQL
+
+      note_metadata1
+      note_metadata2
+      note_metadata3
+      note_metadata4
+      note_metadata5
+
+      system_note_metadata.connection.execute(<<~SQL)
+        ALTER TABLE system_note_metadata
+          ADD CONSTRAINT check_9135b6f0b6 CHECK (namespace_id IS NOT NULL) NOT VALID;
+
+        ALTER TABLE system_note_metadata ENABLE TRIGGER ALL;
+      SQL
+    end
+
+    it 'updates records in batches' do
+      expect do
+        migrate
+      end.to make_queries_matching(/UPDATE\s+"system_note_metadata"/, 3)
+    end
+
+    it 'sets correct namespace_id in every record' do
+      expect { migrate }.to change { note_metadata1.reload.namespace_id }.from(nil).to(project_namespace1.id).and(
+        change { note_metadata2.reload.namespace_id }.from(nil).to(project_namespace2.id)
+      ).and(
+        change { note_metadata3.reload.namespace_id }.from(nil).to(group_namespace1.id)
+      ).and(
+        change { note_metadata4.reload.namespace_id }.from(nil).to(group_namespace2.id)
+      ).and(
+        not_change { note_metadata5.reload.namespace_id }.from(project_namespace1.id)
+      ).and(
+        change { note_metadata6.reload.namespace_id }.from(group_namespace2.id).to(project_namespace2.id)
+      )
+    end
+  end
+  # rubocop:enable RSpec/MultipleMemoizedHelpers
+end
diff --git a/spec/migrations/20251021184303_queue_backfill_system_note_metadata_namespace_id_spec.rb b/spec/migrations/20251021184303_queue_backfill_system_note_metadata_namespace_id_spec.rb
new file mode 100644
index 0000000000000000000000000000000000000000..164ffe6b5be0c59aa2fef45a475767ba49162560
--- /dev/null
+++ b/spec/migrations/20251021184303_queue_backfill_system_note_metadata_namespace_id_spec.rb
@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+require 'spec_helper'
+require_migration!
+
+RSpec.describe QueueBackfillSystemNoteMetadataNamespaceId, migration: :gitlab_main_org, feature_category: :team_planning 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_org,
+          table_name: :system_note_metadata,
+          column_name: :id,
+          batch_size: described_class::BATCH_SIZE,
+          sub_batch_size: described_class::SUB_BATCH_SIZE
+        )
+      }
+    end
+  end
+end