[GitHub integration] [GitHub integration] Claude GitHub MCP Connector authenticates successfully but cannot access private repositories

Screenshot

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What were you trying to do?

What's Wrong?

Claude.ai can authenticate successfully to my GitHub account through the Claude Github MCP Connector, but the connector cannot access my private repositories.

GitHub account:
TtomSt

Private repository:
TtomSt/dentflow

Public repository used for comparison:
TtomSt/ai-advisory-board

The public repository works correctly.

The private repository does not.

When Claude uses the GitHub integration:

• authentication succeeds as TtomSt
• TtomSt/ai-advisory-board is visible and readable
• TtomSt/dentflow returns 404 Not Found
• repository search only returns the public repository
• the private repository is invisible to the runtime connector

The issue is specific to private repository access.

Important GitHub App state

GitHub shows:

Claude Github MCP Connector
Owned by anthropics

The app is listed under:
GitHub Settings → Applications → Authorized GitHub Apps

Its permissions page shows that it can:

• Verify my GitHub identity
• Know what resources I can access
• Act on my behalf

But GitHub also explicitly shows:

"Claude Github MCP Connector has not been installed on any accounts you have access to."

The Claude Github MCP Connector does NOT appear under:
GitHub Settings → Applications → Installed GitHub Apps

This appears to be the key problem.

The connector is authorized at user level, but it has no GitHub App installation on my personal account, so it cannot access private repositories.

Separate Claude Code GitHub App

There is also a separate GitHub App called:

Claude

That app IS installed on my TtomSt account.

It is the Claude Code GitHub App and GitHub describes it as:

"Run Claude Code from your GitHub Pull Requests and Issues..."

It currently has:

Repository access:
All repositories

Permissions include read/write access to code and other repository resources.

This app is separate from the Claude Github MCP Connector.

GitHub explicitly states on the MCP connector page:

"This app is separate from the Claude App used by Claude Code for security purposes."

Therefore, the installed Claude Code GitHub App does not appear to provide private repository access to the Claude.ai GitHub MCP connector.

Claude.ai behavior

In Claude.ai:

1. I open a new chat
2. Click +
3. Select "Add from GitHub"
4. Claude can see TtomSt/dentflow in the repository picker
5. I select the repository and branch main
6. Claude inserts the repository URL into the chat
7. When Claude tries to use the GitHub integration to read the repository, it cannot access it

When explicitly instructed:

"Use GitHub for this"

Claude reports:

• authentication works
• signed in as TtomSt
• reading TtomSt/dentflow fails with 404
• the repository is not visible to the connection
• repository search only returns TtomSt/ai-advisory-board

Public repo:
TtomSt/ai-advisory-board
WORKS

Private repo:
TtomSt/dentflow
FAILS

What I have already tried

I have already tried:

• disconnecting and reconnecting the GitHub connector in Claude.ai
• revoking and reauthorizing Claude Github MCP Connector
• starting fresh Claude chats
• using + → Add from GitHub
• selecting TtomSt/dentflow directly
• selecting branch main
• explicitly asking Claude to use the GitHub integration
• verifying the private repository exists and is accessible normally in GitHub
• verifying the repository is owned by the same GitHub account, TtomSt
• verifying the separate Claude Code GitHub App has All repositories access

The issue persists.

What Should Happen?

After authenticating the Claude Github MCP Connector and selecting TtomSt/dentflow through "Add from GitHub", Claude.ai should be able to read:

• repository root
• files
• folders
• branches
• file contents

through the authenticated GitHub integration.

The connector should have access to private repositories that the authenticated GitHub user owns and has permission to access.

Actual Behavior

The connector can:

• authenticate me successfully
• identify me as TtomSt
• read public repositories

But it cannot:

• see private repositories
• list TtomSt/dentflow
• read any files from TtomSt/dentflow

Private repository requests return 404.

Steps to Reproduce

1. Use a personal GitHub account with a private repository
2. In Claude.ai, connect GitHub
3. Authorize Claude Github MCP Connector
4. Open a new Claude chat
5. Click + → Add from GitHub
6. Select a private repository
7. Add the repository to the chat
8. Ask Claude to read the repository through GitHub
9. Claude authenticates successfully
10. Private repository returns 404 or is invisible
11. Public repositories on the same account remain readable

Suspected Cause

The Claude Github MCP Connector is authorized but not installed.

GitHub explicitly reports:

"Claude Github MCP Connector has not been installed on any accounts you have access to."

This suggests the Claude.ai GitHub MCP connection flow completes user authorization but does not create or attach the GitHub App installation required for private repository access.

This may explain why public repositories work while private repositories return 404.

Related Existing Reports

This appears similar to existing reports where:

• private personal repositories are visible in the picker
• public repositories work
• private repositories cannot be read
• reconnecting does not fix the problem

Related issues include:

#91416
#79083

Diagnostics

Filed from:
GitHub settings for Claude Code on claude.ai

Report code:
GH-WDUUK8

Page:
claude.ai/customize/connectors/integration-github

Client:
web

Environment

Claude:
claude.ai web

GitHub account type:
Personal account

GitHub username:
TtomSt

Operating system:
Windows

Browser:
Desktop web browser

Private repository:
TtomSt/dentflow

Public comparison repository:
TtomSt/ai-advisory-board

Additional Evidence

I can provide screenshots showing:

1. Claude Github MCP Connector under Authorized GitHub Apps
2. Claude Github MCP Connector permissions
3. The message:

"Claude Github MCP Connector has not been installed on any accounts you have access to."

1. Installed GitHub Apps showing that only the separate Claude Code GitHub App is installed
2. Claude.ai successfully authenticating as TtomSt
3. Public repository access working
4. Private repository TtomSt/dentflow returning 404

Please investigate whether the Claude Github MCP Connector installation is missing or failing to attach to my personal GitHub account.

If this requires a backend repository access reset, connector re-provisioning, or GitHub App installation repair, please apply that to GitHub account:

TtomSt

What happened instead?

<img width="664" height="329" alt="Image" src="https://github.com/user-attachments/assets/7eaff46e-b0c7-45c8-9c36-889c90043acd" />
<img width="642" height="337" alt="Image" src="https://github.com/user-attachments/assets/ceb554f2-6e9a-40ab-8a72-1032fbb1171f" />

Diagnostics

Filed from: GitHub settings for Claude Code on claude.ai
Report code: GH-WDUUK8
Page: claude.ai/customize/connectors/integration-github
Client: web