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Use Amazon Q Developer’s MCP configuration to register GitHub’s official server as either a local STDIO process or a remote HTTP endpoint. In the IDE, open the MCP tools configuration, choose a scope, map GitHub’s command or URL into Amazon Q’s fields, authenticate with OAuth or a least-privilege personal access token (PAT), and then confirm that the tools appear. In the CLI, add the server to the agent configuration and run /tools.
Choose the connection model first
Amazon Q Developer supports MCP servers in both its IDE integrations and CLI. GitHub’s official server can run locally with Docker or a built Go binary, which Q starts through STDIO. A remote MCP deployment is accessed over HTTP and may require authorization.
| Decision | Use this when | Trade-off |
|---|---|---|
| IDE or CLI | IDE for visual setup and per-tool approvals; CLI for agent configuration and terminal sessions | IDE is easier to inspect; CLI is easier to reproduce in scripts and projects |
| STDIO or HTTP | STDIO for a process on your computer; HTTP for an already-hosted endpoint | STDIO needs Docker or a local binary; HTTP needs a reachable URL and authorization |
| Global or local scope | Global for reuse across projects; local for one workspace | Workspace-level settings take precedence over global settings |
| OAuth or PAT | OAuth for browser-based sign-in; PAT for explicit, managed credentials | OAuth avoids placing a token in configuration; PAT handling and permissions become your responsibility |
GitHub’s README cautions that MCP host configuration syntax varies. Do not paste a configuration file written for another MCP client into Amazon Q unchanged; use Q’s own fields and put GitHub’s command, arguments, URL, headers, and environment values into those fields.
Prepare GitHub’s official MCP server
Option A: run the published Docker image
Install Docker and ensure your account can run containers. GitHub publishes the image ghcr.io/github/github-mcp-server. A typical STDIO launch with a PAT is:
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docker run -i --rm
-e GITHUB_PERSONAL_ACCESS_TOKEN
ghcr.io/github/github-mcp-serverWhen Amazon Q launches this process, it communicates over standard input and output. Keep diagnostic output out of the protocol stream and make sure Docker is available on the same machine as Q.
Option B: build and run the Go binary
If Docker is not suitable, build the server from GitHub’s repository according to its current instructions, then start the binary in STDIO mode:
github-mcp-server stdioExpose authentication to the process through the environment rather than committing a token to a project file:
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export GITHUB_PERSONAL_ACCESS_TOKEN='replace-with-your-token'
github-mcp-server stdioGitHub Enterprise Server and ghe.com can require a different application or host setup. Follow GitHub’s Enterprise instructions for the server version and host you operate.
Connect it in the Amazon Q IDE
- Open MCP configuration. In your IDE, open the Amazon Q panel, open Chat, and select the tools icon to reach MCP configuration.
- Add a server. Choose global to make the server available across projects, or local to restrict it to the current workspace. Q stores global settings in
~/.aws/amazonq/default.jsonand local settings in.amazonq/default.json. Workspace configuration wins when both exist. Legacymcp.jsonlocations are supported when the documented compatibility setting is enabled. - Select the transport. Choose STDIO for Docker or the local binary. Enter the executable in the command field, such as
dockerorgithub-mcp-server, then add the image,runflags, orstdioargument in the arguments field. PutGITHUB_PERSONAL_ACCESS_TOKENin the environment-variable section if you are using a PAT. - Configure HTTP when using a hosted server. Select HTTP, enter the endpoint URL, and add any required headers. Q can open a browser authorization page when the endpoint requires supported authorization.
- Save and review permissions. Q attempts to connect after you save. For each exposed tool, choose Ask, Always allow, or Deny. Use Ask first while you learn what the server can do.
Example STDIO field mapping
| Amazon Q field | Docker value | Binary value |
|---|---|---|
| Command | docker |
github-mcp-server |
| Arguments | run -i --rm -e GITHUB_PERSONAL_ACCESS_TOKEN ghcr.io/github/github-mcp-server |
stdio |
| Environment | GITHUB_PERSONAL_ACCESS_TOKEN=… |
GITHUB_PERSONAL_ACCESS_TOKEN=… |
The table shows how to translate the server launch into Q’s separate fields; it is not a portable JSON schema. Q’s labels and supported options can change between IDE releases.
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Authenticate safely
OAuth
GitHub’s official README documents OAuth for the local GitHub.com server image. The first use opens a browser login flow and keeps the resulting token in memory. For Docker OAuth, GitHub documents publishing the callback on loopback port 8085. Ensure that port is reachable from the browser completing the flow.
Personal access token
Set GITHUB_PERSONAL_ACCESS_TOKEN in the server environment. GitHub states that a PAT takes precedence over OAuth. Keep it outside source control, shell history where possible, and shared workspace files. Grant only the GitHub permissions required by the toolsets you enable.
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Limit the GitHub tools before using them
The server groups capabilities into toolsets. GitHub documents these defaults: context, repos, issues, pull_requests, and users. Select narrower groups with the server’s --toolsets option or the GITHUB_TOOLSETS environment variable.
Least-privilege examples
- Repository browsing only: enable
contextandrepos. - Issue triage: add
issues; do not enable pull-request tools unless needed. - Pull-request maintenance: add
pull_requestsand retain only the repository context required. - User lookups: enable
usersonly when the workflow genuinely needs them.
Toolsets reduce the surface Q can discover, while Q’s Ask/Always allow/Deny controls determine whether a particular call can run. Treat write-capable operations as Ask until you have reviewed their behavior.
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Configure Amazon Q Developer CLI
Q CLI stores MCP servers in agent configuration. The exact file shape is version-dependent, so use the CLI commands and current Q configuration reference rather than copying another host’s JSON.
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- Add a local process with
qchat mcp add, supplying the server name, command, arguments, and environment values requested by your installed version. - For a remote endpoint, configure a server with
type: "http"and its URL in the agent configuration. - Use
qchat mcp listto confirm the registration. Useqchat mcp statusfor connection state,qchat mcp removeto delete an entry, andqchat mcp importwhen importing a supported configuration. - Start or resume a session. For a remote OAuth server, run
/mcpand complete authorization while the session is active. - Run
/tools. Q initializes servers in the background and lists tools as each server finishes loading.
If initialization is slow, increase the CLI timeout with q settings mcp.initTimeout [value], using a value appropriate for your network and server startup time.
Verify that the connection works
- In the IDE, check the MCP panel for a connected state and inspect the exposed tool list.
- In CLI, run
/toolsand wait for all servers to finish loading. - Ask Q for a read-only operation such as listing repositories you can access. Confirm that the result matches your GitHub account.
- Test one intentionally restricted capability. If its tool is absent, your toolset filter is working.
- Only after verification, change selected tools from Ask to Always allow where the risk is acceptable.
Troubleshoot common failures
Q reports a connection problem
Reopen the server entry and check the executable, arguments, Docker image name, HTTP URL, headers, environment variables, and timeout. For STDIO, run the exact command in a terminal first. For HTTP, test reachability from the same network where Q runs.
No tools appear
Wait for background initialization, then run CLI /tools again. A server can be connected while its tools are still loading. If the list remains empty, inspect toolset filters and server logs.
Authentication never starts
For IDE HTTP connections, verify that the endpoint supports the authorization method Q expects and that the URL is exact. For CLI OAuth, keep the session open while running /mcp. For local OAuth in Docker, verify the loopback callback publication on port 8085.
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Docker OAuth callback fails
Check that the browser can reach the callback published by the container on loopback port 8085. A container that cannot publish that port cannot complete the documented flow.
The PAT is rejected or too powerful
Confirm the variable name is exactly GITHUB_PERSONAL_ACCESS_TOKEN, then review token permissions and enabled toolsets. Replace broad access with the smallest repository and operation scope that satisfies the workflow.
Copied configuration JSON does not work
Configuration formats differ between MCP hosts. Recreate the entry using Amazon Q’s command, arguments, environment, URL, and header fields instead of pasting a file designed for another client.
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Frequently Asked Questions
Can I use both OAuth and a PAT at the same time?
Yes, but GitHub documents that GITHUB_PERSONAL_ACCESS_TOKEN takes precedence over OAuth, so remove or unset the variable when you want to test the OAuth path.
Where should a shared team configuration live?
Use a global Q configuration only when every project should inherit the server. Keep repository-specific settings local, because workspace configuration takes precedence and limits accidental exposure.
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Check the selected GitHub toolsets first. A deliberately excluded tool will not appear in Q; a server that is still initializing may appear only after background loading completes.
The Bottom Line
Connect GitHub to Amazon Q by mapping the official server’s Docker or binary command into Q’s STDIO fields, or by entering a remote HTTP endpoint. Authenticate with OAuth or a least-privilege PAT, restrict toolsets, approve tools conservatively, and verify discovery with the IDE panel or CLI /tools.
Quick Recap
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