diff --git a/api/src/channel/channel.service.ts b/api/src/channel/channel.service.ts
index 00c987c00..3ddf04082 100644
--- a/api/src/channel/channel.service.ts
+++ b/api/src/channel/channel.service.ts
@@ -6,13 +6,18 @@
  * 2. All derivative works must include clear attribution to the original creator and software, Hexastack and Hexabot, in a prominent location (e.g., in the software's "About" section, documentation, and README file).
  */
 
-import { Injectable, UnauthorizedException } from '@nestjs/common';
+import {
+  Injectable,
+  OnApplicationBootstrap,
+  UnauthorizedException,
+} from '@nestjs/common';
 import { Request, Response } from 'express';
 
 import { SubscriberService } from '@/chat/services/subscriber.service';
 import { CONSOLE_CHANNEL_NAME } from '@/extensions/channels/console/settings';
 import { WEB_CHANNEL_NAME } from '@/extensions/channels/web/settings';
 import { LoggerService } from '@/logger/logger.service';
+import { SettingService } from '@/setting/services/setting.service';
 import { getSessionStore } from '@/utils/constants/session-store';
 import {
   SocketGet,
@@ -27,14 +32,42 @@ import ChannelHandler from './lib/Handler';
 import { ChannelName } from './types';
 
 @Injectable()
-export class ChannelService {
+export class ChannelService implements OnApplicationBootstrap {
   private registry: Map<string, ChannelHandler<ChannelName>> = new Map();
 
   constructor(
     private readonly logger: LoggerService,
+    private readonly settingService: SettingService,
     private readonly subscriberService: SubscriberService,
   ) {}
 
+  async onApplicationBootstrap(): Promise<void> {
+    await this.cleanup();
+  }
+
+  /**
+   * Cleanups the unregisterd channels from settings.
+   *
+   */
+  async cleanup(): Promise<void> {
+    const activePlugins = this.getAll().map((handler) =>
+      handler.getNamespace(),
+    );
+
+    const channelSettings = (await this.settingService.getAllGroups()).filter(
+      (group) => group.split('_').pop() === 'channel',
+    ) as HyphenToUnderscore<ChannelName>[];
+
+    const orphanSettings = channelSettings.filter(
+      (group) => !activePlugins.includes(group),
+    );
+
+    for (const group of orphanSettings) {
+      this.logger.log(`Deleting orphaned settings for ${group}...`);
+      await this.settingService.deleteGroup(group);
+    }
+  }
+
   /**
    * Registers a channel with a specific handler.
    *
diff --git a/api/src/extra/index.ts b/api/src/extra/index.ts
index 1c6f0b7d0..d773e1360 100644
--- a/api/src/extra/index.ts
+++ b/api/src/extra/index.ts
@@ -1,18 +1,9 @@
 /*
- * Copyright © 2025 Hexastack. All rights reserved.
+ * Copyright © 2024 Hexastack. All rights reserved.
  *
  * Licensed under the GNU Affero General Public License v3.0 (AGPLv3) with the following additional terms:
  * 1. The name "Hexabot" is a trademark of Hexastack. You may not use this name in derivative works without express written permission.
  * 2. All derivative works must include clear attribution to the original creator and software, Hexastack and Hexabot, in a prominent location (e.g., in the software's "About" section, documentation, and README file).
  */
 
-import { Module } from '@nestjs/common';
-
-import { CleanupService } from './cleanup.service';
-
-@Module({
-  providers: [CleanupService],
-})
-class CleanupModule {}
-
-export default [CleanupModule];
+export default [];
diff --git a/api/src/helper/helper.service.ts b/api/src/helper/helper.service.ts
index db0a88008..285784923 100644
--- a/api/src/helper/helper.service.ts
+++ b/api/src/helper/helper.service.ts
@@ -6,7 +6,11 @@
  * 2. All derivative works must include clear attribution to the original creator and software, Hexastack and Hexabot, in a prominent location (e.g., in the software's "About" section, documentation, and README file).
  */
 
-import { Injectable, InternalServerErrorException } from '@nestjs/common';
+import {
+  Injectable,
+  InternalServerErrorException,
+  OnApplicationBootstrap,
+} from '@nestjs/common';
 
 import { LoggerService } from '@/logger/logger.service';
 import { SettingService } from '@/setting/services/setting.service';
@@ -15,7 +19,7 @@ import BaseHelper from './lib/base-helper';
 import { HelperName, HelperRegistry, HelperType, TypeOfHelper } from './types';
 
 @Injectable()
-export class HelperService {
+export class HelperService implements OnApplicationBootstrap {
   private registry: HelperRegistry = new Map();
 
   constructor(
@@ -28,6 +32,33 @@ export class HelperService {
     });
   }
 
+  async onApplicationBootstrap(): Promise<void> {
+    await this.cleanup();
+  }
+
+  /**
+   * Cleanups the unregisterd helpers from settings.
+   *
+   */
+  async cleanup(): Promise<void> {
+    const activeHelpers = this.getAll().map((handler) =>
+      handler.getNamespace(),
+    );
+
+    const helperSettings = (await this.settingService.getAllGroups()).filter(
+      (group) => group.split('_').pop() === 'helper',
+    ) as HyphenToUnderscore<HelperName>[];
+
+    const orphanSettings = helperSettings.filter(
+      (group) => !activeHelpers.includes(group),
+    );
+
+    for (const group of orphanSettings) {
+      this.logger.log(`Deleting orphaned settings for ${group}...`);
+      await this.settingService.deleteGroup(group);
+    }
+  }
+
   /**
    * Registers a helper.
    *
diff --git a/api/src/plugins/plugins.service.ts b/api/src/plugins/plugins.service.ts
index 8a2667c94..51edc39e7 100644
--- a/api/src/plugins/plugins.service.ts
+++ b/api/src/plugins/plugins.service.ts
@@ -6,7 +6,14 @@
  * 2. All derivative works must include clear attribution to the original creator and software, Hexastack and Hexabot, in a prominent location (e.g., in the software's "About" section, documentation, and README file).
  */
 
-import { Injectable, InternalServerErrorException } from '@nestjs/common';
+import {
+  Injectable,
+  InternalServerErrorException,
+  OnApplicationBootstrap,
+} from '@nestjs/common';
+
+import { LoggerService } from '@/logger/logger.service';
+import { SettingService } from '@/setting/services/setting.service';
 
 import { BasePlugin } from './base-plugin.service';
 import { PluginInstance } from './map-types';
@@ -26,7 +33,9 @@ import { PluginName, PluginType } from './types';
  * @typeparam T - The plugin type, which extends from `BasePlugin`. By default, it uses `BaseBlockPlugin`.
  */
 @Injectable()
-export class PluginService<T extends BasePlugin = BasePlugin> {
+export class PluginService<T extends BasePlugin = BasePlugin>
+  implements OnApplicationBootstrap
+{
   /**
    * The registry of plugins, stored as a map where the first key is the type of plugin,
    * the second key is the name of the plugin and the value is a plugin of type `T`.
@@ -35,7 +44,37 @@ export class PluginService<T extends BasePlugin = BasePlugin> {
     Object.keys(PluginType).map((t) => [t as PluginType, new Map()]),
   );
 
-  constructor() {}
+  constructor(
+    private readonly settingService: SettingService,
+    private readonly logger: LoggerService,
+  ) {}
+
+  async onApplicationBootstrap(): Promise<void> {
+    await this.cleanup();
+  }
+
+  /**
+   * Cleanups the unregisterd plugins from settings.
+   *
+   */
+  async cleanup(): Promise<void> {
+    const activePlugins = this.getAll().map((handler) =>
+      handler.getNamespace(),
+    );
+
+    const pluginSettings = (await this.settingService.getAllGroups()).filter(
+      (group) => group.split('_').pop() === 'plugin',
+    ) as HyphenToUnderscore<PluginName>[];
+
+    const orphanSettings = pluginSettings.filter(
+      (group) => !activePlugins.includes(group),
+    );
+
+    for (const group of orphanSettings) {
+      this.logger.log(`Deleting orphaned settings for ${group}...`);
+      await this.settingService.deleteGroup(group);
+    }
+  }
 
   /**
    * Registers a plugin with a given name.