mongodb-mcp-setup

SKILL.md

MongoDB MCP Server Setup

This skill guides users through configuring the MongoDB MCP server for use with an agentic client.

Overview

The MongoDB MCP server requires authentication. Users have three options:

Connection String (Option A): Direct connection to a specific cluster

Quick setup for single cluster

Requires MDB_MCP_CONNECTION_STRING environment variable

Service Account Credentials (Option B): MongoDB Atlas Admin API access

Recommended for Atlas users - simplifies authentication and data access

Access to Atlas Admin API and dynamic cluster connection via atlas-connect-cluster

No manual DB user credential management

Requires MDB_MCP_API_CLIENT_ID and MDB_MCP_API_CLIENT_SECRET environment variables

Atlas Local (Option C): Local development with Docker

Best for local testing - zero configuration required

Runs Atlas locally in Docker, requires Docker installed

No credentials or cloud cluster access

This is an interactive step-by-step guide. The agent detects the user's environment and provides tailored instructions, but never asks for or handles credentials — users add those directly to their shell profile or agentic client config in Step 5. Make this clear to the user whenever credentials come up in Steps 3a and 3b.

Step 0: Detect Client

Before anything else, determine which agentic client the user is running. This controls how credentials are configured in Step 1 and Step 5.

Run:

env | grep "^CODEX_"

If no CODEX_* variables are present → the user is running a shell-based client (Claude, Cursor, Gemini CLI, Copilot CLI, etc.). Credentials are configured via shell profile environment variables.

If any CODEX_* variables are present → the user is running Codex. Credentials are stored in ~/.codex/config.toml (macOS/Linux) or %USERPROFILE%\.codex\config.toml (Windows), not in shell environment variables. The desktop app does not inherit shell env vars when launched from Finder, Launchpad, or the Windows Start menu.

Carry this client type (Codex vs. shell-based) forward through every subsequent step.

Step 1: Check Existing Configuration

Check whether credentials are already configured.

For shell-based clients — check the current environment:

env | grep "^MDB_MCP" | sed '/^MDB_MCP_READ_ONLY=/!s/=.*/=[set]/'

For Codex — search ~/.codex/config.toml (macOS/Linux) or %USERPROFILE%\.codex\config.toml (Windows):

grep -E 'MDB_MCP_(CONNECTION_STRING|API_CLIENT_ID|API_CLIENT_SECRET|READ_ONLY)' ~/.codex/config.toml 2>/dev/null | sed '/MDB_MCP_READ_ONLY/!s/[[:space:]]*=[[:space:]].*/ = "[set]"/'

Interpretation (both):

If MDB_MCP_CONNECTION_STRING appears → connection string auth is configured

If both MDB_MCP_API_CLIENT_ID and MDB_MCP_API_CLIENT_SECRET appear → service account auth is configured. If only one is present, treat it as incomplete.

If MDB_MCP_READ_ONLY appears → read-only mode is enabled

Partial Configuration Handling:

User wants to add read-only to existing setup (has auth, no read-only flag) → skip to Step 4

User wants to switch authentication methods → explain they should remove the old credentials first (from config.toml for Codex, from their shell profile for shell-based clients), then proceed with Steps 2–5

User wants to update credentials → skip to Step 5

Important: If the user wants an Atlas Admin API action (managing clusters, creating users, performance advisor) but only has MDB_MCP_CONNECTION_STRING, explain they need service account credentials and offer to walk through setup.

Step 2: Present Configuration Options

If no valid configuration exists, present the options:

Connection String (Option A) — Best for:

Single cluster access

Existing database credentials

Self-hosted MongoDB or no Atlas Admin API needs

Service Account Credentials (Option B) — Best for:

MongoDB Atlas users (recommended)

Multi-cluster switching

Atlas Admin API access (cluster management, user creation, performance monitoring)

Atlas Local (Option C) — Best for:

Local development/testing without cloud setup

Fastest setup with Docker, no credentials required

Ask the user which option they'd like to proceed with.

Step 3a: Connection String Setup

If the user chooses Option A:

3a.1: Explain How to Find the Connection String

Explain where and how to obtain their connection string:

For MongoDB Atlas:

Go to cloud.mongodb.com

Select your cluster → click Connect

Choose Drivers or Shell → copy the connection string

Replace <username> and <password> with your database user credentials

For self-hosted MongoDB:

The connection string is typically configured by your DBA or in your application config

Format: mongodb://username:password@host:port/database

Expected formats:

mongodb://username:password@host:port/database

mongodb+srv://username:password@cluster.mongodb.net/database

mongodb://host:port (local, no auth)

Proceed to Step 4 (Determine Read-Only Access).

Step 3b: Service Account Setup

If the user chooses Option B:

3b.1: Guide Through Atlas Service Account Creation

Direct the user to create a MongoDB Atlas Service Account:

Full documentation: https://www.mongodb.com/docs/mcp-server/prerequisites/

Walk them through the key steps:

Navigate to MongoDB Atlas — cloud.mongodb.com

Select your organization from the ORGANIZATION section near the top of the page

Go to "Project Identity and Access" on the left sidebar → Applications → Create Service Account

Set Permissions — Grant Organization Member or Project Owner (see docs for exact permission mappings)

Generate Credentials — Create Client ID and Secret

⚠️ The Client Secret is shown only once — save it immediately before leaving the page

Note both values — you'll need Client ID and Client Secret for Step 5

3b.2: API Access List Configuration

⚠️ CRITICAL: The user MUST add their IP address to the service account's API Access List, or all Atlas Admin API operations will fail.

Steps:

On the service account details page, find API Access List

Click Add Access List Entry

Add your current IP address. Use a specific IP or CIDR range whenever possible.

⚠️ 0.0.0.0/0 allows access from any IP — this is a significant security risk. Only use it as a last resort for temporary testing and remove it immediately afterward. It should never be used in production.

Save changes

This is more secure than global Network Access settings as it only affects API access, not database connections.

Proceed to Step 4 (Determine Read-Only Access).

Step 3c: Atlas Local Setup

If the user chooses Option C:

3c.1: Check Docker Installation

Verify Docker is installed:

docker info

If not installed, direct them to: https://www.docker.com/get-started

3c.2: Confirm Setup Complete

Atlas Local requires no credentials — the user is ready to go:

Create deployments: atlas-local-create-deployment

List deployments: atlas-local-list-deployments

All operations work out of the box with Docker

Skip Steps 4 and 5 (no configuration needed) and proceed to Step 6 (Next Steps).

Step 4: Determine Read-Only vs Read-Write Access

Only applies to Options A and B. Skip to Step 6 for Option C.

Ask whether they want read-only or read-write access:

Read-Write (default): Full data access, modifications allowed

Best for: Development, testing, administrative tasks

Read-Only: Data reads only, no modifications

Best for: Production data safety, reporting, compliance

If read-only: include the read-only flag in the credential snippet in Step 5.
If read-write: omit it (defaults to read-write).

Proceed to Step 5 (Configure Credentials).

Step 5: Configure Credentials

Do not ask for or handle credentials — provide exact instructions so the user can add them directly.

5.1: Add credentials

For shell-based clients — store credentials in a dedicated ~/.mcp-env file (not directly in the shell profile), then source it from the profile. This keeps credentials out of files that are often group/world readable by default and prevents accidentally committing them to git.

For Codex — add to ~/.codex/config.toml (macOS/Linux) or %USERPROFILE%\.codex\config.toml (Windows).

Show the user the appropriate snippet:

For Connection String (Option A):

Shell-based clients (~/.mcp-env):

export MDB_MCP_CONNECTION_STRING="<paste-your-connection-string-here>"

Codex (config.toml):

[mcp_servers.mongodb.env]
MDB_MCP_CONNECTION_STRING = "<paste-your-connection-string-here>"

For Service Account (Option B):

Shell-based clients (~/.mcp-env):

export MDB_MCP_API_CLIENT_ID="<paste-your-client-id-here>"
export MDB_MCP_API_CLIENT_SECRET="<paste-your-client-secret-here>"

Codex (config.toml):

[mcp_servers.mongodb.env]
MDB_MCP_API_CLIENT_ID = "<paste-your-client-id-here>"
MDB_MCP_API_CLIENT_SECRET = "<paste-your-client-secret-here>"

If read-only was chosen (Step 4), also add:

Shell-based: export MDB_MCP_READ_ONLY="true" in ~/.mcp-env.

Codex: MDB_MCP_READ_ONLY = "true" under the same [mcp_servers.mongodb.env] section.

⚠️ Both config.toml and ~/.mcp-env are stored in plaintext. Do not commit them to version control.

5.2: Finalize (shell-based clients only)

Restrict permissions on ~/.mcp-env:

# adjust for windows if needed
chmod 600 ~/.mcp-env

Add source ~/.mcp-env to the shell profile (e.g. ~/.zshrc). Adjust for the detected shell (e.g. for fish: bass source ~/.mcp-env or set -x; for PowerShell: dot-source a .ps1 file instead).

Detect the shell and profile file by running echo $SHELL if needed.

5.3: Verify

Shell-based clients — reload the profile first, then verify:

source ~/.zshrc  # adjust to match the profile file
env | grep "^MDB_MCP" | sed '/^MDB_MCP_READ_ONLY=/!s/=.*/=[set]/'

Codex:

# adjust path if on Windows
grep -E 'MDB_MCP_(CONNECTION_STRING|API_CLIENT_ID|API_CLIENT_SECRET|READ_ONLY)' ~/.codex/config.toml 2>/dev/null | sed '/MDB_MCP_READ_ONLY/!s/[[:space:]]*=[[:space:]].*/ = "[set]"/'

Expected output shows the configured key(s) with values redacted to [set]. If nothing appears, check that credentials were saved and (for shell-based clients) that the profile was reloaded.

Proceed to Step 6 (Next Steps).

Step 6: Next Steps

For Options A & B (Connection String / Service Account):

Restart the agentic client:

Shell-based clients: Fully quit the client, then run source <profile-file> to load the new variables, and reopen the client from that same terminal session so it inherits the environment.

Codex: Fully quit and relaunch the app. No terminal session needed — credentials come from config.toml.

Verify MCP Server: After restart, test by performing a MongoDB operation.

Using the Tools:

Option A: Direct database access tools available

Option B: Additionally has Atlas Admin API tools and atlas-connect-cluster

Important (Option B): Ensure your IP is in the service account's API Access List or all API calls will fail

For Option C (Atlas Local):

Ready to use: No restart or configuration needed!

Next steps:

Create deployments: atlas-local-create-deployment

List deployments: atlas-local-list-deployments

Use standard database operations once connected

Troubleshooting

Variables not appearing after source (shell-based clients): Check the profile file path and confirm the file was saved

Client doesn't pick up variables: Ensure full restart (quit + reopen), not just a reload

Codex desktop app not picking up credentials: If launched from Finder, Launchpad, or the Windows Start menu, Codex does not inherit shell environment variables from .zshrc/.zprofile/PowerShell profiles. Use ~/.codex/config.toml (macOS/Linux) or %USERPROFILE%\.codex\config.toml (Windows) instead (see Step 5)

Invalid connection string format: Re-check the format; must start with mongodb:// or mongodb+srv://

Atlas Admin API errors (Option B): Verify your IP is in the service account's API Access List

Read-only mode not working: Check that MDB_MCP_READ_ONLY is set — in config.toml under [mcp_servers.mongodb.env] for Codex, or via env | grep ^MDB_MCP_READ_ONLY for shell-based clients

fish/PowerShell: Syntax differs — use set -x (fish) or $env: (PowerShell) instead of export