diff --git a/docs/telemetry-events.md b/docs/telemetry-events.md
index 01c2d66ca83a9..4165dc42a2e4e 100644
--- a/docs/telemetry-events.md
+++ b/docs/telemetry-events.md
@@ -2813,6 +2813,17 @@ void
 }
 ```
 
+### mcp/uninstall/duplicate
+
+> Sent when a duplicate manual MCP installation is uninstalled
+
+```typescript
+{
+  'app': string,
+  'source': 'account' | 'subscription' | 'graph' | 'composer' | 'patchDetails' | 'settings' | 'timeline' | 'home' | 'ai' | 'ai:markdown-preview' | 'ai:markdown-editor' | 'ai:picker' | 'associateIssueWithBranch' | 'cloud-patches' | 'code-suggest' | 'commandPalette' | 'deeplink' | 'editor:hover' | 'feature-badge' | 'feature-gate' | 'gk-cli-integration' | 'gk-mcp-provider' | 'inspect' | 'inspect-overview' | 'integrations' | 'launchpad' | 'launchpad-indicator' | 'launchpad-view' | 'mcp' | 'mcp-welcome-message' | 'merge-target' | 'notification' | 'prompt' | 'quick-wizard' | 'rebaseEditor' | 'remoteProvider' | 'scm' | 'scm-input' | 'startWork' | 'trial-indicator' | 'view' | 'walkthrough' | 'whatsnew' | 'worktrees'
+}
+```
+
 ### openReviewMode
 
 > Sent when a PR review was started in the inspect overview
diff --git a/src/constants.telemetry.ts b/src/constants.telemetry.ts
index 1622d10ea6e0a..025dea7be6672 100644
--- a/src/constants.telemetry.ts
+++ b/src/constants.telemetry.ts
@@ -254,6 +254,8 @@ export interface TelemetryEvents extends WebviewShowAbortedEvents, WebviewShownE
 	'mcp/setup/failed': MCPSetupFailedEvent;
 	/** Sent when GitKraken MCP registration fails */
 	'mcp/registration/failed': MCPSetupFailedEvent;
+	/** Sent when a duplicate manual MCP installation is uninstalled */
+	'mcp/uninstall/duplicate': MCPUninstallDuplicateEvent;
 
 	/** Sent when a PR review was started in the inspect overview */
 	openReviewMode: OpenReviewModeEvent;
@@ -526,6 +528,11 @@ export interface MCPSetupFailedEvent {
 	'error.message'?: string;
 }
 
+export interface MCPUninstallDuplicateEvent {
+	app: string;
+	source: Sources;
+}
+
 interface CloudIntegrationsConnectingEvent {
 	'integration.ids': string | undefined;
 }
diff --git a/src/env/node/gk/mcp/integration.ts b/src/env/node/gk/mcp/integration.ts
index a2458ee19770b..c28503bbd9694 100644
--- a/src/env/node/gk/mcp/integration.ts
+++ b/src/env/node/gk/mcp/integration.ts
@@ -1,5 +1,5 @@
 import type { Event, McpServerDefinition, McpServerDefinitionProvider } from 'vscode';
-import { Disposable, env, EventEmitter, lm, McpStdioServerDefinition } from 'vscode';
+import { Disposable, env, EventEmitter, lm, McpStdioServerDefinition, Uri, workspace } from 'vscode';
 import type { Container } from '../../../../container';
 import type { StorageChangeEvent } from '../../../../system/-webview/storage';
 import { getHostAppName } from '../../../../system/-webview/vscode';
@@ -95,6 +95,9 @@ export class GkMcpProvider implements McpServerDefinitionProvider, Disposable {
 			return undefined;
 		}
 
+		// Clean up any duplicate manual installations before registering the bundled version
+		await this.removeDuplicateManualMcpConfigurations();
+
 		let output = await runCLICommand(['mcp', 'config', appName, '--source=gitlens', `--scheme=${env.uriScheme}`], {
 			cwd: cliPath,
 		});
@@ -120,6 +123,119 @@ export class GkMcpProvider implements McpServerDefinitionProvider, Disposable {
 		return undefined;
 	}
 
+	@debug()
+	private async removeDuplicateManualMcpConfigurations(): Promise<void> {
+		try {
+			// Use globalStorageUri to locate the User folder where settings.json is stored
+			// globalStorageUri points to: .../[AppName]/User/globalStorage/eamodio.gitlens
+			// Going up 2 levels gets us to: .../[AppName]/User/
+			const globalStorageUri = this.container.context.globalStorageUri;
+			const userFolderUri = Uri.joinPath(globalStorageUri, '..', '..');
+			const settingsUri = Uri.joinPath(userFolderUri, 'settings.json');
+			
+			// Check if settings file exists
+			try {
+				await workspace.fs.stat(settingsUri);
+			} catch {
+				// Settings file doesn't exist, nothing to clean up
+				Logger.debug(`Settings file does not exist: ${settingsUri.fsPath}`);
+				return;
+			}
+
+			// Read and parse settings file
+			const settingsBytes = await workspace.fs.readFile(settingsUri);
+			const settingsText = new TextDecoder().decode(settingsBytes);
+			
+			// Parse JSON with comments support (VS Code settings.json allows comments)
+			const settings = this.parseJsonWithComments(settingsText);
+			
+			// Check for MCP server configurations
+			const mcpServersKey = 'languageModels.chat.mcpServers';
+			if (!settings[mcpServersKey] || typeof settings[mcpServersKey] !== 'object') {
+				Logger.debug('No MCP server configurations found');
+				return;
+			}
+
+			const mcpServers = settings[mcpServersKey] as Record<string, unknown>;
+			let removedCount = 0;
+			const serversToRemove: string[] = [];
+
+			// Look for GitKraken MCP servers that were manually installed
+			// These typically have names like "gitkraken" or "GitKraken" and contain
+			// the GK CLI executable path
+			for (const [serverName, serverConfig] of Object.entries(mcpServers)) {
+				if (this.isGitKrakenMcpServer(serverName, serverConfig)) {
+					serversToRemove.push(serverName);
+					Logger.log(`Found duplicate manual MCP configuration: ${serverName}`);
+				}
+			}
+
+			// Remove the servers
+			for (const serverName of serversToRemove) {
+				mcpServers[serverName] = undefined;
+				removedCount++;
+			}
+
+			if (removedCount === 0) {
+				Logger.debug('No duplicate manual MCP configurations found');
+				return;
+			}
+
+			// Save updated settings
+			const updatedSettingsText = JSON.stringify(settings, null, '\t');
+			await workspace.fs.writeFile(settingsUri, new TextEncoder().encode(updatedSettingsText));
+
+			Logger.log(`Removed ${removedCount} duplicate manual MCP configuration(s) from ${settingsUri.fsPath}`);
+
+			if (this.container.telemetry.enabled) {
+				this.container.telemetry.sendEvent('mcp/uninstall/duplicate', {
+					app: settingsUri.fsPath,
+					source: 'gk-mcp-provider',
+				});
+			}
+		} catch (ex) {
+			// Log error but don't fail the overall process
+			Logger.error(`Error removing duplicate MCP configurations: ${ex}`);
+		}
+	}
+
+	private parseJsonWithComments(text: string): Record<string, unknown> {
+		// Simple JSON comment remover - removes // and /* */ comments
+		// This is a simplified version; VS Code uses jsonc-parser for full support
+		const withoutComments = text
+			.replace(/\/\*[\s\S]*?\*\//g, '') // Remove /* */ comments
+			.replace(/\/\/.*/g, ''); // Remove // comments
+
+		return JSON.parse(withoutComments) as Record<string, unknown>;
+	}
+
+	private isGitKrakenMcpServer(serverName: string, serverConfig: unknown): boolean {
+		// Check if this is a GitKraken MCP server by looking for:
+		// 1. Server name matches GitKraken variants
+		// 2. Command contains 'gk' executable
+		// 3. Args contain '--source=gitlens' or scheme parameter
+		
+		const nameMatches = /^git[_-]?kraken$/i.test(serverName);
+		
+		if (typeof serverConfig !== 'object' || serverConfig == null) {
+			return false;
+		}
+
+		const config = serverConfig as Record<string, unknown>;
+		const command = typeof config.command === 'string' ? config.command : '';
+		const args = Array.isArray(config.args) ? config.args : [];
+		
+		// Check if command contains gk executable
+		const commandMatches = command.includes('/gk') || command.includes('\\gk') || command.endsWith('gk.exe');
+		
+		// Check if args contain source=gitlens
+		const argsMatch = args.some((arg: unknown) => 
+			typeof arg === 'string' && arg.includes('--source=gitlens')
+		);
+
+		return nameMatches && commandMatches && argsMatch;
+	}
+
 	private onRegistrationCompleted(_cliVersion?: string | undefined) {
 		if (!this.container.telemetry.enabled) return;