GitHub MCP Server Tools Not Working in Copilot Spaces When Used in VS Code

[HelenLyuRey]

GitHub MCP Server Searching Tools Not Working in Copilot Spaces When Used in VS Code

Component Overview

This issue involves the interaction between three distinct components:

1. GitHub MCP Server - The MCP server searching tools such as #search_repositories, or even build-in tools #githubRepo
2. GitHub Copilot Spaces - Configured AI assistants with custom instructions and tool access on web version
3. VS Code IDE - with GitHub Copilot extension integration

The bug occurs specifically when all three components are used together: GitHub MCP search tools fail to execute when invoked through a Copilot Space within VS Code, despite working correctly in other combinations.

Environment Information

Required System Details:

• VS Code version: 1.105.1
• GitHub Copilot extension version: 1.388.0
• Operating System: Windows 11 Pro Editional with Version 24H2
• Network environment: Hong Kong Internet Without VPN

Describe the bug

GitHub MCP Server tools (specifically #search_repositories/ #githubRepo, any tools about code searching in github) fail when used within a GitHub Copilot Space in VS Code, displaying "The GitHub code search index is not yet available". This is an integration-specific issue, as the same tools work correctly in isolation or different combinations of the three components.

Working vs Non-Working Scenarios

✅ What works:

• GitHub MCP tools used directly in VS Code Copilot Chat (bypassing Copilot Space)

• Same Copilot Space with GitHub MCP tools works in web version of GitHub Copilot

• Other MCP tools (e.g., Atlassian MCP) work fine in Copilot Spaces within VS Code

❌ What doesn't work:

• GitHub MCP tools specifically when used through Copilot Spaces in VS Code
• Issue has persisted for 3+ days, ruling out temporary connectivity issues

Steps to reproduce the behavior

1. Create a GitHub Copilot Space named "GitHub Code Assistant" with instructions that include GitHub MCP tools like #search_repositories

2. Open VS Code and access the Copilot Space through VS Code Copilot Chat
3. Attempt to use the space to search for code (e.g., "search for MFT integration code")
4. Observe the error: "The GitHub code search index is not yet available"

Expected vs actual behavior

Expected behavior: The GitHub Copilot Space should successfully execute GitHub MCP Server tools in VS Code, maintaining consistency with the web version functionality.

Actual behavior:

• Error message: "The GitHub code search index is not yet available"
• No search results are returned
• Functionality works in web version but fails in VS Code

Timeline and Impact

Timeline:

• Issue started approximately 3-4 days ago (around October 27-28, 2025)
• Was working correctly as of last week
• Consistent reproduction across multiple attempts

Impact: This prevents using specialized Copilot Spaces for GitHub code search in VS Code, forcing users to either use the less-integrated web version or manually invoke MCP tools without space-specific context.

Workaround

Currently using direct MCP tool invocation in VS Code Copilot Chat as a workaround, but this defeats the purpose of having a configured Copilot Space for specialized GitHub code search functionality.

Questions and Next Steps

This issue raises several important questions about the GitHub MCP Server and Copilot Spaces integration:

Root Cause Analysis:

• What changes were deployed in the past week (around October 27-28, 2025) that might have introduced this regression?
• Are there known compatibility issues between specific versions of GitHub MCP Server and VS Code Copilot integration?

Product Roadmap and Priorities:

• Given that Copilot Spaces integration with VS Code is still in early stages, what is the expected timeline for stability improvements?
• What priority level will this integration bug receive, considering it affects a core workflow for developers using GitHub MCP tools?

User Experience Improvements:

• Are there plans to add a space selection interface for user in VS Code Copilot Chat, similar to the Agent mode selection?
• Currently, space routing appears inconsistent - sometimes using the configured space, other times defaulting to general tool routing. Will there be improvements to make this behavior more predictable and user-controlled?

Request: Please provide visibility into the development roadmap for these integrations and any other workarounds or beta features that might address these workflow challenges while permanent fixes are being developed.

[helen-share-collab]

I also encountered this problem.

[chutiA12]

https://github.com/github/github-mcp-server/issues/1343