Local MCP servers silently ignored when Claude Desktop installed from Microsoft Store

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Problem
Local MCP servers configured in %APPDATA%\Claude\claude_desktop_config.json are silently ignored when Claude Desktop is installed from the Microsoft Store. The Developer settings page shows "No servers added" despite a valid config file in the correct location.
Symptoms

Config file at %APPDATA%\Claude\claude_desktop_config.json is present, valid JSON, and contains a properly structured mcpServers block
Developer settings page shows "No servers added"
"Edit Config" button opens the correct file in the correct location
No error messages, no MCP-related logs — the config is simply not read
The MCP package itself works fine when run manually from the command line (npx -y @houtini/google-knowledge-graph-mcp)
Node.js is installed and npx is in PATH

What Should Happen?

Claude Desktop should launch MCP servers based on config.

Error Messages/Logs

The only log present was %LOCALAPPDATA%\Claude\Logs\chrome-native-host.log, which contained exclusively Chrome native messaging host entries — no MCP server loading activity at all. This indicated the app was running as a Chromium-based PWA/Store app rather than the standalone Electron app.
Confirming the installed binary:
where /R "%LOCALAPPDATA%" claude.exe
Returned:
C:\Program Files\WindowsApps\Claude_1.1.2998.0_x64__pzs8sxrjxfjjc\app\claude.exe
This is the Microsoft Store (MSIX) package. Also found multiple failed Squirrel installer remnants in %LOCALAPPDATA%\SquirrelTemp\ from prior attempts to install the direct-download version, which apparently did not complete successfully while the Store version was present.

Steps to Reproduce

1. Install Claude Desktop from Microsoft Store
2. Subsequently update by downloading from Claude site directly. Removing app from Settings/Apps in Windows alone does not fix.
3. Attempt to connect to an MCP server.

Resolution

1. Downloaded the standalone installer directly from [claude.ai/download] (https://claude.ai/download) (Squirrel/Electron version, not the Microsoft Store)
2. Cleaned up failed prior install attempts: rd /s /q "%LOCALAPPDATA%\SquirrelTemp"
3. Uninstalled the Microsoft Store version via Windows Settings → Apps
4. Installed the direct-download version
5. Launched — MCP server loaded immediately from the existing config file, no changes needed

Suggestion

• The Microsoft Store version should either support local MCP servers via claude_desktop_config.json or surface a clear message in Developer settings that local MCP servers are not supported in the Store edition.
• The "Edit Config" button in the Store version is misleading — it opens and lets you edit a config file that the app never reads.
• Documentation for MCP setup should note that the Microsoft Store version does not support local MCP servers.

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

Version 1.1.2998 (1f1d4d)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_