diff --git a/apps/desktop/src/main/mutations/files/file-delete.ts b/apps/desktop/src/main/mutations/files/file-delete.ts
index 815eb21a..f8de1f5c 100644
--- a/apps/desktop/src/main/mutations/files/file-delete.ts
+++ b/apps/desktop/src/main/mutations/files/file-delete.ts
@@ -1,9 +1,13 @@
-import { entryService } from '@/main/services/entry-service';
+import { DeleteFileMutationData, generateId, IdType } from '@colanode/core';
+
+import { databaseService } from '@/main/data/database-service';
 import { MutationHandler } from '@/main/types';
 import {
   FileDeleteMutationInput,
   FileDeleteMutationOutput,
 } from '@/shared/mutations/files/file-delete';
+import { eventBus } from '@/shared/lib/event-bus';
+import { mapFile } from '@/main/utils';
 
 export class FileDeleteMutationHandler
   implements MutationHandler<FileDeleteMutationInput>
@@ -11,7 +15,55 @@ export class FileDeleteMutationHandler
   async handleMutation(
     input: FileDeleteMutationInput
   ): Promise<FileDeleteMutationOutput> {
-    await entryService.deleteEntry(input.fileId, input.userId);
+    const workspaceDatabase = await databaseService.getWorkspaceDatabase(
+      input.userId
+    );
+
+    const file = await workspaceDatabase
+      .selectFrom('files')
+      .selectAll()
+      .where('id', '=', input.fileId)
+      .executeTakeFirst();
+
+    if (!file) {
+      return {
+        success: true,
+      };
+    }
+
+    const deletedAt = new Date().toISOString();
+    const deleteFileMutationData: DeleteFileMutationData = {
+      id: input.fileId,
+      rootId: file.root_id,
+      deletedAt,
+    };
+
+    await workspaceDatabase.transaction().execute(async (tx) => {
+      await tx.deleteFrom('files').where('id', '=', input.fileId).execute();
+
+      await tx
+        .insertInto('mutations')
+        .values({
+          id: generateId(IdType.Mutation),
+          type: 'delete_file',
+          node_id: input.fileId,
+          data: JSON.stringify(deleteFileMutationData),
+          created_at: deletedAt,
+          retries: 0,
+        })
+        .execute();
+    });
+
+    eventBus.publish({
+      type: 'file_deleted',
+      userId: input.userId,
+      file: mapFile(file),
+    });
+
+    eventBus.publish({
+      type: 'mutation_created',
+      userId: input.userId,
+    });
 
     return {
       success: true,
diff --git a/apps/desktop/src/main/mutations/messages/message-delete.ts b/apps/desktop/src/main/mutations/messages/message-delete.ts
index fa27c9c0..62362621 100644
--- a/apps/desktop/src/main/mutations/messages/message-delete.ts
+++ b/apps/desktop/src/main/mutations/messages/message-delete.ts
@@ -1,9 +1,13 @@
-import { entryService } from '@/main/services/entry-service';
+import { DeleteMessageMutationData, generateId, IdType } from '@colanode/core';
+
+import { databaseService } from '@/main/data/database-service';
 import { MutationHandler } from '@/main/types';
 import {
   MessageDeleteMutationInput,
   MessageDeleteMutationOutput,
 } from '@/shared/mutations/messages/message-delete';
+import { eventBus } from '@/shared/lib/event-bus';
+import { mapMessage } from '@/main/utils';
 
 export class MessageDeleteMutationHandler
   implements MutationHandler<MessageDeleteMutationInput>
@@ -11,7 +15,58 @@ export class MessageDeleteMutationHandler
   async handleMutation(
     input: MessageDeleteMutationInput
   ): Promise<MessageDeleteMutationOutput> {
-    await entryService.deleteEntry(input.messageId, input.userId);
+    const workspaceDatabase = await databaseService.getWorkspaceDatabase(
+      input.userId
+    );
+
+    const message = await workspaceDatabase
+      .selectFrom('messages')
+      .selectAll()
+      .where('id', '=', input.messageId)
+      .executeTakeFirst();
+
+    if (!message) {
+      return {
+        success: true,
+      };
+    }
+
+    const deletedAt = new Date().toISOString();
+    const deleteMessageMutationData: DeleteMessageMutationData = {
+      id: input.messageId,
+      rootId: message.root_id,
+      deletedAt,
+    };
+
+    await workspaceDatabase.transaction().execute(async (tx) => {
+      await tx
+        .deleteFrom('messages')
+        .where('id', '=', input.messageId)
+        .execute();
+
+      await tx
+        .insertInto('mutations')
+        .values({
+          id: generateId(IdType.Mutation),
+          type: 'delete_message',
+          node_id: input.messageId,
+          data: JSON.stringify(deleteMessageMutationData),
+          created_at: deletedAt,
+          retries: 0,
+        })
+        .execute();
+    });
+
+    eventBus.publish({
+      type: 'message_deleted',
+      userId: input.userId,
+      message: mapMessage(message),
+    });
+
+    eventBus.publish({
+      type: 'mutation_created',
+      userId: input.userId,
+    });
 
     return {
       success: true,
diff --git a/apps/desktop/src/main/services/file-service.ts b/apps/desktop/src/main/services/file-service.ts
index 8fc1cabe..d0a44381 100644
--- a/apps/desktop/src/main/services/file-service.ts
+++ b/apps/desktop/src/main/services/file-service.ts
@@ -442,6 +442,46 @@ class FileService {
     const workspaceDatabase =
       await databaseService.getWorkspaceDatabase(userId);
 
+    if (file.deletedAt) {
+      const deletedFile = await workspaceDatabase
+        .deleteFrom('files')
+        .returningAll()
+        .where('id', '=', file.id)
+        .executeTakeFirst();
+
+      if (!deletedFile) {
+        return;
+      }
+
+      await workspaceDatabase
+        .deleteFrom('file_interactions')
+        .where('file_id', '=', file.id)
+        .execute();
+
+      await workspaceDatabase
+        .deleteFrom('file_states')
+        .where('file_id', '=', file.id)
+        .execute();
+
+      // if the file exists in the workspace, we need to delete it
+      const filePath = path.join(
+        getWorkspaceFilesDirectoryPath(userId),
+        `${file.id}${file.extension}`
+      );
+
+      if (fs.existsSync(filePath)) {
+        fs.rmSync(filePath, { force: true });
+      }
+
+      eventBus.publish({
+        type: 'file_deleted',
+        userId,
+        file: mapFile(deletedFile),
+      });
+
+      return;
+    }
+
     const existingFile = await workspaceDatabase
       .selectFrom('files')
       .selectAll()
diff --git a/apps/desktop/src/main/services/message-service.ts b/apps/desktop/src/main/services/message-service.ts
index 979b65ad..f43a6b98 100644
--- a/apps/desktop/src/main/services/message-service.ts
+++ b/apps/desktop/src/main/services/message-service.ts
@@ -21,6 +21,41 @@ class MessageService {
     const workspaceDatabase =
       await databaseService.getWorkspaceDatabase(userId);
 
+    if (message.deletedAt) {
+      const deletedMessage = await workspaceDatabase
+        .deleteFrom('messages')
+        .returningAll()
+        .where('id', '=', message.id)
+        .executeTakeFirst();
+
+      if (!deletedMessage) {
+        return;
+      }
+
+      await workspaceDatabase
+        .deleteFrom('message_reactions')
+        .where('message_id', '=', message.id)
+        .execute();
+
+      await workspaceDatabase
+        .deleteFrom('message_interactions')
+        .where('message_id', '=', message.id)
+        .execute();
+
+      await workspaceDatabase
+        .deleteFrom('texts')
+        .where('id', '=', message.id)
+        .execute();
+
+      eventBus.publish({
+        type: 'message_deleted',
+        userId,
+        message: mapMessage(deletedMessage),
+      });
+
+      return;
+    }
+
     const existingMessage = await workspaceDatabase
       .selectFrom('messages')
       .selectAll()
diff --git a/apps/server/src/controllers/client/workspaces/mutations/mutations-sync.ts b/apps/server/src/controllers/client/workspaces/mutations/mutations-sync.ts
index d43c0233..911e6dcc 100644
--- a/apps/server/src/controllers/client/workspaces/mutations/mutations-sync.ts
+++ b/apps/server/src/controllers/client/workspaces/mutations/mutations-sync.ts
@@ -16,6 +16,8 @@ import {
   MarkMessageSeenMutation,
   MarkFileSeenMutation,
   MarkFileOpenedMutation,
+  DeleteFileMutation,
+  DeleteMessageMutation,
 } from '@colanode/core';
 
 import { SelectUser } from '@/data/schema';
@@ -62,8 +64,12 @@ const handleMutation = async (
     return await handleDeleteTransaction(user, mutation);
   } else if (mutation.type === 'create_file') {
     return await handleCreateFile(user, mutation);
+  } else if (mutation.type === 'delete_file') {
+    return await handleDeleteFile(user, mutation);
   } else if (mutation.type === 'create_message') {
     return await handleCreateMessage(user, mutation);
+  } else if (mutation.type === 'delete_message') {
+    return await handleDeleteMessage(user, mutation);
   } else if (mutation.type === 'create_message_reaction') {
     return await handleCreateMessageReaction(user, mutation);
   } else if (mutation.type === 'delete_message_reaction') {
@@ -148,6 +154,14 @@ const handleCreateFile = async (
   return output ? 'success' : 'error';
 };
 
+const handleDeleteFile = async (
+  user: SelectUser,
+  mutation: DeleteFileMutation
+): Promise<SyncMutationStatus> => {
+  const output = await fileService.deleteFile(user, mutation);
+  return output ? 'success' : 'error';
+};
+
 const handleCreateMessage = async (
   user: SelectUser,
   mutation: CreateMessageMutation
@@ -156,6 +170,14 @@ const handleCreateMessage = async (
   return output ? 'success' : 'error';
 };
 
+const handleDeleteMessage = async (
+  user: SelectUser,
+  mutation: DeleteMessageMutation
+): Promise<SyncMutationStatus> => {
+  const output = await messageService.deleteMessage(user, mutation);
+  return output ? 'success' : 'error';
+};
+
 const handleCreateMessageReaction = async (
   user: SelectUser,
   mutation: CreateMessageReactionMutation
diff --git a/apps/server/src/services/file-service.ts b/apps/server/src/services/file-service.ts
index ae1631e1..2f51cb12 100644
--- a/apps/server/src/services/file-service.ts
+++ b/apps/server/src/services/file-service.ts
@@ -1,5 +1,6 @@
 import {
   CreateFileMutation,
+  DeleteFileMutation,
   extractEntryRole,
   FileStatus,
   hasCollaboratorAccess,
@@ -78,6 +79,60 @@ class FileService {
     return true;
   }
 
+  public async deleteFile(
+    user: SelectUser,
+    mutation: DeleteFileMutation
+  ): Promise<boolean> {
+    const file = await database
+      .selectFrom('files')
+      .selectAll()
+      .where('id', '=', mutation.data.id)
+      .executeTakeFirst();
+
+    if (!file) {
+      return true;
+    }
+
+    const root = await database
+      .selectFrom('entries')
+      .selectAll()
+      .where('id', '=', mutation.data.rootId)
+      .executeTakeFirst();
+
+    if (!root) {
+      return false;
+    }
+
+    const rootEntry = mapEntry(root);
+    const role = extractEntryRole(rootEntry, user.id);
+    if (!hasCollaboratorAccess(role)) {
+      return false;
+    }
+
+    const deletedFile = await database
+      .updateTable('files')
+      .returningAll()
+      .set({
+        deleted_at: new Date(mutation.data.deletedAt),
+        deleted_by: user.id,
+      })
+      .where('id', '=', mutation.data.id)
+      .executeTakeFirst();
+
+    if (!deletedFile) {
+      return false;
+    }
+
+    eventBus.publish({
+      type: 'file_deleted',
+      fileId: deletedFile.id,
+      rootId: deletedFile.root_id,
+      workspaceId: deletedFile.workspace_id,
+    });
+
+    return true;
+  }
+
   public async markFileAsSeen(
     user: SelectUser,
     mutation: MarkFileSeenMutation
diff --git a/apps/server/src/services/message-service.ts b/apps/server/src/services/message-service.ts
index ae45b924..a357783f 100644
--- a/apps/server/src/services/message-service.ts
+++ b/apps/server/src/services/message-service.ts
@@ -1,6 +1,7 @@
 import {
   CreateMessageMutation,
   CreateMessageReactionMutation,
+  DeleteMessageMutation,
   DeleteMessageReactionMutation,
   extractEntryRole,
   hasCollaboratorAccess,
@@ -73,6 +74,60 @@ class MessageService {
     return true;
   }
 
+  public async deleteMessage(
+    user: SelectUser,
+    mutation: DeleteMessageMutation
+  ): Promise<boolean> {
+    const message = await database
+      .selectFrom('messages')
+      .select(['id', 'root_id', 'workspace_id'])
+      .where('id', '=', mutation.data.id)
+      .executeTakeFirst();
+
+    if (!message) {
+      return true;
+    }
+
+    const root = await database
+      .selectFrom('entries')
+      .selectAll()
+      .where('id', '=', message.root_id)
+      .executeTakeFirst();
+
+    if (!root) {
+      return false;
+    }
+
+    const rootEntry = mapEntry(root);
+    const role = extractEntryRole(rootEntry, user.id);
+    if (!hasCollaboratorAccess(role)) {
+      return false;
+    }
+
+    const deletedMessage = await database
+      .updateTable('messages')
+      .returningAll()
+      .set({
+        deleted_at: new Date(mutation.data.deletedAt),
+        deleted_by: user.id,
+      })
+      .where('id', '=', mutation.data.id)
+      .executeTakeFirst();
+
+    if (!deletedMessage) {
+      return false;
+    }
+
+    eventBus.publish({
+      type: 'message_deleted',
+      messageId: deletedMessage.id,
+      rootId: deletedMessage.root_id,
+      workspaceId: deletedMessage.workspace_id,
+    });
+
+    return true;
+  }
+
   public async createMessageReaction(
     user: SelectUser,
     mutation: CreateMessageReactionMutation
diff --git a/packages/core/src/types/mutations.ts b/packages/core/src/types/mutations.ts
index ba353f95..d034fed1 100644
--- a/packages/core/src/types/mutations.ts
+++ b/packages/core/src/types/mutations.ts
@@ -45,6 +45,17 @@ export type CreateFileMutation = MutationBase & {
   data: CreateFileMutationData;
 };
 
+export type DeleteFileMutationData = {
+  id: string;
+  rootId: string;
+  deletedAt: string;
+};
+
+export type DeleteFileMutation = MutationBase & {
+  type: 'delete_file';
+  data: DeleteFileMutationData;
+};
+
 export type ApplyCreateTransactionMutation = MutationBase & {
   type: 'apply_create_transaction';
   data: LocalCreateTransaction;
@@ -75,6 +86,17 @@ export type CreateMessageMutation = MutationBase & {
   data: CreateMessageMutationData;
 };
 
+export type DeleteMessageMutationData = {
+  id: string;
+  rootId: string;
+  deletedAt: string;
+};
+
+export type DeleteMessageMutation = MutationBase & {
+  type: 'delete_message';
+  data: DeleteMessageMutationData;
+};
+
 export type CreateMessageReactionMutationData = {
   messageId: string;
   reaction: string;
@@ -156,10 +178,12 @@ export type MarkEntryOpenedMutation = MutationBase & {
 
 export type Mutation =
   | CreateFileMutation
+  | DeleteFileMutation
   | ApplyCreateTransactionMutation
   | ApplyUpdateTransactionMutation
   | ApplyDeleteTransactionMutation
   | CreateMessageMutation
+  | DeleteMessageMutation
   | CreateMessageReactionMutation
   | DeleteMessageReactionMutation
   | MarkMessageSeenMutation