diff --git a/meet-ce/backend/src/repositories/base.repository.ts b/meet-ce/backend/src/repositories/base.repository.ts
index dae5a43e..ac5b8949 100644
--- a/meet-ce/backend/src/repositories/base.repository.ts
+++ b/meet-ce/backend/src/repositories/base.repository.ts
@@ -35,6 +35,16 @@ export abstract class BaseRepository<TDomain, TDocument extends TDomain = TDomai
 		return [];
 	}
 
+	/**
+	 * Returns document paths that must be updated atomically.
+	 *
+	 * Paths listed here are treated as leaf values during partial updates,
+	 * so nested properties are not flattened into dot notation.
+	 */
+	protected getAtomicUpdatePaths(): readonly string[] {
+		return [];
+	}
+
 	/**
 	 * Creates a new document.
 	 *
@@ -338,6 +348,7 @@ export abstract class BaseRepository<TDomain, TDocument extends TDomain = TDomai
 	protected buildUpdateQuery(partial: Partial<TDocument>): UpdateQuery<TDocument> {
 		const $set: Record<string, unknown> = {};
 		const $unset: Record<string, ''> = {};
+		const atomicUpdatePaths = new Set(this.getAtomicUpdatePaths());
 
 		const buildUpdateQueryDeep = (input: Record<string, unknown>, prefix = ''): void => {
 			for (const key in input) {
@@ -347,8 +358,8 @@ export abstract class BaseRepository<TDomain, TDocument extends TDomain = TDomai
 				if (value === undefined) {
 					// Mark field for unsetting if value is undefined
 					$unset[path] = '';
-				} else if (this.isPlainObject(value)) {
-					// Recursively build update query for nested objects
+				} else if (this.isPlainObject(value) && !atomicUpdatePaths.has(path)) {
+					// Recursively build update query for nested objects that are not atomic paths
 					buildUpdateQueryDeep(value, path);
 				} else {
 					// Set field value for $set operator
diff --git a/meet-ce/backend/src/repositories/recording.repository.ts b/meet-ce/backend/src/repositories/recording.repository.ts
index 20072bac..f4acf29e 100644
--- a/meet-ce/backend/src/repositories/recording.repository.ts
+++ b/meet-ce/backend/src/repositories/recording.repository.ts
@@ -38,6 +38,12 @@ export class RecordingRepository extends BaseRepository<MeetRecordingInfo, MeetR
 		return MEET_RECORDING_DOCUMENT_ONLY_FIELDS;
 	}
 
+	protected override getAtomicUpdatePaths(): readonly string[] {
+		// Recording encoding must be treated as an atomic update path because
+		// it can be either a string or an object, and we want to ensure it is fully replaced rather than partially updated.
+		return ['encoding'];
+	}
+
 	/**
 	 * Creates a new recording with generated access secrets.
 	 *
diff --git a/meet-ce/backend/src/repositories/room.repository.ts b/meet-ce/backend/src/repositories/room.repository.ts
index 4cc34a19..8cb9d22f 100644
--- a/meet-ce/backend/src/repositories/room.repository.ts
+++ b/meet-ce/backend/src/repositories/room.repository.ts
@@ -40,6 +40,12 @@ export class RoomRepository extends BaseRepository<MeetRoom, MeetRoomDocument> {
 		return MEET_ROOM_DOCUMENT_ONLY_FIELDS;
 	}
 
+	protected override getAtomicUpdatePaths(): readonly string[] {
+		// Recording encoding must be treated as an atomic update path because
+		// it can be either a string or an object, and we want to ensure it is fully replaced rather than partially updated.
+		return ['config.recording.encoding'];
+	}
+
 	/**
 	 * Creates a new room.
 	 * URLs are stored in the database without the base URL.
diff --git a/meet-ce/backend/tests/integration/api/rooms/expired-rooms-gc.test.ts b/meet-ce/backend/tests/integration/api/rooms/expired-rooms-gc.test.ts
index ba4cdcc5..54c8d28f 100644
--- a/meet-ce/backend/tests/integration/api/rooms/expired-rooms-gc.test.ts
+++ b/meet-ce/backend/tests/integration/api/rooms/expired-rooms-gc.test.ts
@@ -98,7 +98,7 @@ describe('Expired Rooms GC Tests', () => {
 		expect(response.body).toHaveProperty('meetingEndAction', 'delete');
 
 		// End the meeting
-		const { moderatorSecret } = MeetRoomHelper.extractSecretsFromRoom(room);
+		const { moderatorSecret } = MeetRoomHelper.extractSecretsFromRoom(room.anonymous);
 		const moderatorToken = await generateRoomMemberToken(room.roomId, { secret: moderatorSecret });
 		await endMeeting(room.roomId, moderatorToken);