This plugin connects Microsoft 365 Copilot Cowork to GitHub through GitHub's official remote MCP server. Once set up, you can read issues, browse code, and open draft pull requests from inside a Cowork conversation, alongside email, files, and Teams context.

Package:

This guide is for the person setting the plugin up for an organization. End users don't need it. There's a handoff message at the bottom you can send them instead.

The package ships unconfigured: its referenceId is a placeholder, and the plugin will not connect until you complete Part 1 below. This is intentional. Your organization registers its own OAuth client, so your users authenticate through credentials you own and control.

How the setup is structured

Three things happen at different scopes. Confusing them is the main source of trouble.

Individual users never touch OAuth and never upload anything. They click Connect and sign in with their own GitHub account, with their own permissions.

Do not have users sideload the package themselves. Cowork enforces one owner per manifest ID per tenant, so the second person to upload it gets:

This manifest ID already belongs to a plugin someone else owns.

Giving each person their own manifest ID "fixes" this, but leaves you with divergent copies you can't update. Admin deployment is the supported path.

Requirements

Part 1: OAuth setup (once per tenant)

GitHub does not support Dynamic Client Registration on its remote MCP server, so Cowork can't create an OAuth client automatically. Each organization registers its own.

Step 1: Create a GitHub OAuth App

GitHub → Settings → Developer settings → OAuth Apps → New OAuth App

Create it under a personal account, not the organization. It still works against org repositories and you won't need org-owner rights.

Copy and paste the callback URL. It's Teams' fixed redirect, identical for every plugin and provider, so never customize it. A mismatch here is a common cause of sign-in failure.

Select Register application, then:

1. Copy the Client ID

2. Select Generate a new client secret and copy it right away, since it's shown only once

Step 2: Register the OAuth client in Teams developer portal

dev.teams.microsoft.com → Tools → OAuth client registration → Register client

Base URL: read this before you continue

Enter the origin only: https://api.githubcopilot.com

Do not enter https://api.githubcopilot.com/mcp/, even though that's the URL in the manifest and Microsoft's documentation says the Base URL "should correspond to" it. Including the path produces:

Connector unavailable. 'GitHub' isn't set up correctly by its publisher: the address its server is registered at doesn't match the one in its sign-in configuration.

The field wants a base that the manifest URL sits underneath. This is verified behaviour and was the single blocking issue during setup.

Other fields worth noting

• Token and Refresh endpoints are the same URL. Correct for GitHub.

• PKCE off. GitHub describes PKCE as upcoming, not current.

• Request body parameters is how GitHub documents its token endpoint. If token exchange fails with an invalid-client error, HTTP Basic is the fallback.

Select Save, then copy the OAuth client registration ID.

Scopes

• repo: read/write issues, PRs, branches, file contents. Required for drafting PRs. It is broad; a GitHub App with fine-grained permissions is the tighter alternative.

• read:org: lets repository listing see organization repositories.

• read:user: backs the account identity check.

Step 3: Put your registration ID in the manifest

Unzip the package, open manifest.json, and replace the placeholder:

json

"authorization": {"type": "OAuthPluginVault","referenceId": "REPLACE_WITH_AUTH_CONFIG_ID"}

Re-zip with all files at the root level, and don't nest them inside a folder:

bash

zip -r github-for-cowork.zip manifest.json color.png outline.png tools/ skills/

powershell

Compress-Archive -Path manifest.json, color.png, outline.png, tools, skills -DestinationPath github-for-cowork.zip

Part 2: Deploy the package (once per tenant)

Requires Teams Administrator, Copilot Administrator, or Global Administrator.

1. Go to admin.microsoft.com

2. Settings → Integrated apps (labelled Agents in some tenants)

3. Select Upload custom apps

4. Upload your configured .zip

5. Assign to Specific users/groups for a first test, or Entire organization

6. Confirm and deploy

Allow a few minutes to propagate.

Before deploying, have anyone who sideloaded the package remove their copy. Two sources for the same manifest ID will conflict.

Admin-deployed plugins appear in users' Sources & Skills automatically, labelled Managed by your organization. Users can't remove them, but can enable or disable them per device.

Part 3: Each user connects (30 seconds)

Admins cannot sign in to GitHub on a user's behalf. Each person authorizes once.

1. Open the plugin in Customize → Plugins → GitHub for Cowork

2. Select Connect next to the GitHub MCP server entry

3. Complete the GitHub sign-in

4. Start a new conversation and send:

set up GitHub

That triggers the setup workflow: confirms which GitHub account was authorized, lists reachable repositories, and asks which repo and base branch to use.

Tool discovery happens at conversation start, so always start a fresh conversation after connecting.

Using it

• "What are the open bugs in my repo?"

• "Read issue 42 and tell me what it's asking for."

• "Turn this email thread into a draft PR."

• "Fix the typo in the README and open a draft pull request."

Safety behaviour

Built into the skill:

• Changes land on new copilot/<description> branches, never the base branch

• Pull requests open as drafts unless the user says otherwise

• Files are read before they're rewritten

• Merging, closing, deleting, and force-pushing are refused

• If the connector is unavailable, the skill says so and stops. It will not substitute a local git repository or recalled details

• Customer names, credentials, and internal URLs are redacted before anything is committed

These are prompt-level conventions, not API-enforced. The connector exposes write tools the skill declines to use, including merge_pull_request and delete_file.

The user's GitHub token permissions are the hard boundary. For a real restriction:

• Scope a fine-grained GitHub token to specific repositories, or

• Set mcpServerUrl to https://api.githubcopilot.com/mcp/readonly, which makes GitHub refuse all write tools server-side, and

• Enable branch protection on your default branch

Cowork also prompts for approval before each write operation.

Optional: pin a default repository

This isn't required, since set up GitHub lets each user pick a repo per conversation. If everyone works in one repo, edit skills/github-repo-workflow/SKILL.md, replace REPLACE_WITH_OWNER / REPLACE_WITH_REPO under Default Repository, and re-zip.

If different people use different repos, leave the placeholders.

Troubleshooting

GitHub organization approval

The most common late-stage blocker. GitHub organizations may block OAuth Apps until an admin approves them; personal repositories are unaffected. Symptom: sign-in succeeds but org repos 403 or don't appear.

An org owner approves at:

https://github.com/organizations/[ORG_NAME]/settings/oauth_application_policy

Members can request approval from the same page.

Copilot Business / Enterprise policy

If the GitHub organization is on Copilot Business or Enterprise, the "MCP servers in Copilot" policy may need enabling. This is documented for Copilot-in-IDE usage; whether it gates other hosts isn't explicitly stated. Worth checking if authorization fails for no other clear reason.

Known constraints

• Requires Streamable HTTP over HTTPS. GitHub's hosted endpoint complies

• API key authentication isn't supported in Cowork; use OAuth

• GitHub Enterprise Server can't use the remote endpoint and needs the self-hosted MCP server. GitHub.com and Enterprise Cloud are fine

• Tenants with Microsoft Purview Information Barriers enabled block plugin uploads entirely

Maintenance

• The GitHub client secret lives in the Microsoft Enterprise token store, never in the package

• Rotating or deleting the GitHub OAuth App breaks the connector for every user at once

• The registration is scoped My organization only. Cross-tenant use requires Any Microsoft 365 organization, and the registration should then be bound to a specific Teams app ID rather than Any Teams app

• Users can revoke their own authorization from Chat settings → Agents

Handoff message for end users

GitHub in Cowork is now available.

It's already installed. You'll find GitHub for Cowork under Sources & Skills.

To start:

1. Open Customize → Plugins → GitHub for Cowork

2. Click Connect and sign in with your GitHub account

3. Start a new conversation and send: set up GitHub

You'll be asked which repository to work in. You're acting as your own GitHub account, so you can only see and change what you normally could.

Changes always go on a new branch, pull requests always open as drafts, and nothing gets merged automatically.