diff --git a/ee/packages/federation-matrix/src/FederationMatrix.ts b/ee/packages/federation-matrix/src/FederationMatrix.ts
index 8339c448c4d7e..e96199b1f48c6 100644
--- a/ee/packages/federation-matrix/src/FederationMatrix.ts
+++ b/ee/packages/federation-matrix/src/FederationMatrix.ts
@@ -4,7 +4,14 @@ import type { PresenceState } from '@hs/core';
 import { ConfigService, createFederationContainer, getAllServices } from '@hs/federation-sdk';
 import type { HomeserverEventSignatures, HomeserverServices, FederationContainerOptions } from '@hs/federation-sdk';
 import { type IFederationMatrixService, Room, ServiceClass, Settings } from '@rocket.chat/core-services';
-import { isDeletedMessage, isMessageFromMatrixFederation, UserStatus, type IMessage, type IRoom, type IUser } from '@rocket.chat/core-typings';
+import {
+	isDeletedMessage,
+	isMessageFromMatrixFederation,
+	UserStatus,
+	type IMessage,
+	type IRoom,
+	type IUser,
+} from '@rocket.chat/core-typings';
 import { Emitter } from '@rocket.chat/emitter';
 import { Router } from '@rocket.chat/http-router';
 import { Logger } from '@rocket.chat/logger';
@@ -20,6 +27,7 @@ import { getMatrixSendJoinRoutes } from './api/_matrix/send-join';
 import { getMatrixTransactionsRoutes } from './api/_matrix/transactions';
 import { getFederationVersionsRoutes } from './api/_matrix/versions';
 import { registerEvents } from './events';
+import { convertExternalUserIdToInternalUsername } from './helpers/identifiers';
 
 export class FederationMatrix extends ServiceClass implements IFederationMatrixService {
 	protected name = 'federation-matrix';
@@ -194,7 +202,7 @@ export class FederationMatrix extends ServiceClass implements IFederationMatrixS
 
 				try {
 					// TODO: Check if it is external user - split domain etc
-					const localUserId = await Users.findOneByUsername(member);
+					const localUserId = await Users.findOneByUsername(convertExternalUserIdToInternalUsername(member));
 					if (localUserId) {
 						await MatrixBridgedUser.createOrUpdateByLocalId(localUserId._id, member, false, matrixDomain);
 						// continue;
@@ -334,8 +342,8 @@ export class FederationMatrix extends ServiceClass implements IFederationMatrixS
 
 					const isExternalUser = username.includes(':');
 					if (isExternalUser) {
-						let externalUsernameToInvite = username;
-						const alreadyCreatedLocally = await Users.findOneByUsername(username, { projection: { _id: 1 } });
+						let externalUsernameToInvite = convertExternalUserIdToInternalUsername(username);
+						const alreadyCreatedLocally = await Users.findOneByUsername(externalUsernameToInvite, { projection: { _id: 1 } });
 						if (alreadyCreatedLocally) {
 							externalUsernameToInvite = `@${username}`;
 						}
diff --git a/ee/packages/federation-matrix/src/events/edu.ts b/ee/packages/federation-matrix/src/events/edu.ts
index 425dcb2de8daf..3fab701075a3c 100644
--- a/ee/packages/federation-matrix/src/events/edu.ts
+++ b/ee/packages/federation-matrix/src/events/edu.ts
@@ -5,8 +5,6 @@ import type { Emitter } from '@rocket.chat/emitter';
 import { Logger } from '@rocket.chat/logger';
 import { MatrixBridgedUser, MatrixBridgedRoom, Users } from '@rocket.chat/models';
 
-import { convertExternalUserIdToInternalUsername } from '../helpers/identifiers';
-
 const logger = new Logger('federation-matrix:edu');
 
 export const edus = async (emitter: Emitter<HomeserverEventSignatures>) => {
@@ -18,7 +16,7 @@ export const edus = async (emitter: Emitter<HomeserverEventSignatures>) => {
 				return;
 			}
 
-			const matrixUser = await MatrixBridgedUser.findOne({ mui: convertExternalUserIdToInternalUsername(data.user_id) });
+			const matrixUser = await MatrixBridgedUser.findOne({ mui: data.user_id });
 			if (!matrixUser) {
 				logger.debug(`No bridged user found for Matrix user_id: ${data.user_id}`);
 				return;
@@ -42,7 +40,7 @@ export const edus = async (emitter: Emitter<HomeserverEventSignatures>) => {
 
 	emitter.on('homeserver.matrix.presence', async (data) => {
 		try {
-			const matrixUser = await MatrixBridgedUser.findOne({ mui: convertExternalUserIdToInternalUsername(data.user_id) });
+			const matrixUser = await MatrixBridgedUser.findOne({ mui: data.user_id });
 			if (!matrixUser) {
 				logger.debug(`No bridged user found for Matrix user_id: ${data.user_id}`);
 				return;
diff --git a/ee/packages/federation-matrix/src/events/message.ts b/ee/packages/federation-matrix/src/events/message.ts
index dfde54bfa158c..f618287e44721 100644
--- a/ee/packages/federation-matrix/src/events/message.ts
+++ b/ee/packages/federation-matrix/src/events/message.ts
@@ -6,6 +6,8 @@ import type { Emitter } from '@rocket.chat/emitter';
 import { Logger } from '@rocket.chat/logger';
 import { Users, MatrixBridgedUser, MatrixBridgedRoom, Rooms, Subscriptions, Messages } from '@rocket.chat/models';
 
+import { convertExternalUserIdToInternalUsername } from '../helpers/identifiers';
+
 const logger = new Logger('federation-matrix:message');
 
 export function message(emitter: Emitter<HomeserverEventSignatures>) {
@@ -29,13 +31,14 @@ export function message(emitter: Emitter<HomeserverEventSignatures>) {
 			}
 			const username = userPart.substring(1);
 
-			let user = await Users.findOneByUsername(data.sender);
+			const internalUsername = convertExternalUserIdToInternalUsername(data.sender);
+			let user = await Users.findOneByUsername(internalUsername);
 
 			if (!user) {
-				logger.info('Creating new federated user:', { username: data.sender, externalId: data.sender });
+				logger.info('Creating new federated user:', { username: internalUsername, externalId: data.sender });
 
 				const userData: Partial<IUser> = {
-					username: data.sender,
+					username: internalUsername,
 					name: username, // TODO: Fetch display name from Matrix profile
 					type: 'user',
 					status: UserStatus.ONLINE,
@@ -58,7 +61,7 @@ export function message(emitter: Emitter<HomeserverEventSignatures>) {
 
 				user = await Users.findOneById(insertedId);
 				if (!user) {
-					logger.error('Failed to create user:', data.sender);
+					logger.error('Failed to create user:', internalUsername);
 					return;
 				}
 
@@ -149,10 +152,10 @@ export function message(emitter: Emitter<HomeserverEventSignatures>) {
 				logger.debug(`No RC message found for event ${data.redacts}`);
 				return;
 			}
-
-			const user = await Users.findOneByUsername(data.sender);
+			const internalUsername = convertExternalUserIdToInternalUsername(data.sender);
+			const user = await Users.findOneByUsername(internalUsername);
 			if (!user) {
-				logger.debug(`User not found: ${data.sender}`);
+				logger.debug(`User not found: ${internalUsername}`);
 				return;
 			}
 
diff --git a/ee/packages/federation-matrix/src/events/reaction.ts b/ee/packages/federation-matrix/src/events/reaction.ts
index a2390f6139ccb..63a0c9bf647ec 100644
--- a/ee/packages/federation-matrix/src/events/reaction.ts
+++ b/ee/packages/federation-matrix/src/events/reaction.ts
@@ -5,6 +5,8 @@ import { Logger } from '@rocket.chat/logger';
 import { Users, Messages } from '@rocket.chat/models'; // Rooms
 import emojione from 'emojione';
 
+import { convertExternalUserIdToInternalUsername } from '../helpers/identifiers';
+
 const logger = new Logger('federation-matrix:reaction');
 
 export function reaction(emitter: Emitter<HomeserverEventSignatures>) {
@@ -21,9 +23,10 @@ export function reaction(emitter: Emitter<HomeserverEventSignatures>) {
 				return;
 			}
 
-			const user = await Users.findOneByUsername(data.sender);
+			const internalUsername = convertExternalUserIdToInternalUsername(data.sender);
+			const user = await Users.findOneByUsername(internalUsername);
 			if (!user) {
-				logger.error(`No RC user mapping found for Matrix event ${reactionTargetEventId} ${data.sender}`);
+				logger.error(`No RC user mapping found for Matrix event ${reactionTargetEventId} ${internalUsername}`);
 				return;
 			}
 
@@ -40,7 +43,7 @@ export function reaction(emitter: Emitter<HomeserverEventSignatures>) {
 
 			const reactionEmoji = emojione.toShort(reactionKey);
 			await Message.reactToMessage(user._id, reactionEmoji, rcMessage._id, true);
-			await Messages.setFederationReactionEventId(data.sender, rcMessage._id, reactionEmoji, data.event_id);
+			await Messages.setFederationReactionEventId(internalUsername, rcMessage._id, reactionEmoji, data.event_id);
 		} catch (error) {
 			logger.error('Failed to process Matrix reaction:', error);
 		}
@@ -75,9 +78,10 @@ export function reaction(emitter: Emitter<HomeserverEventSignatures>) {
 				return;
 			}
 
-			const user = await Users.findOneByUsername(data.sender);
+			const internalUsername = convertExternalUserIdToInternalUsername(data.sender);
+			const user = await Users.findOneByUsername(internalUsername);
 			if (!user) {
-				logger.debug(`User not found: ${data.sender}`);
+				logger.debug(`User not found: ${internalUsername}`);
 				return;
 			}