Official agent skill

Mongodb MCP Setup

by mongodb in mongodb/agent-skills

Guide users through configuring key MongoDB MCP server options.

OfficialApache-2.0Auto-check passedDatabases

Install Mongodb MCP Setup

skills CLI
$ npx skills add mongodb/agent-skills --skill mongodb-mcp-setup -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install mongodb/agent-skills mongodb-mcp-setup --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/mongodb/agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/mongodb-mcp-setup .claude/skills/mongodb-mcp-setup && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
mongodb-mcp-setup
GitHub stars
190
Used in
1 other repo
Token cost
~3.3k tokens
SKILL.md length
1,531 words
Files
1
Skills in repo
9
Repo updated
First seen
Licence
Apache-2.0

At a glance

Guide users through configuring key MongoDB MCP server options.

  • Works in 6 steps: Detect Client → Check Existing Configuration → Present Configuration Options → …
  • A user has the MongoDB MCP server installed but hasnt configured the required environment variables
  • SKILL.md covers Overview, Step 0: Detect Client, Step 1: Check Existing… and Step 2: Present Configuration…, plus 7 more sections
  • Calls docker; needs MDB_MCP_API_CLIENT_SECRET and API_CLIENT_SECRET

What it does

Mongodb MCP Setup is an agent skill from mongodb/agent-skills, published by the product's own GitHub organization. Guide users through configuring key MongoDB MCP server options. Use this skill when a user has the MongoDB MCP server installed but hasn't configured the required environment variables, or when they ask about connecting to MongoDB/Atlas and don't have the credentials set up.

Its SKILL.md is about 3.3k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Databases, covering NoSQL databases, MCP servers and Secrets management. It works with MongoDB, Model Context Protocol and Docker. The repository describes itself as: Use the official MongoDB Skills with your favorite coding agent to build faster. The licence is Apache-2.0.

When your agent uses it

  • A user has the MongoDB MCP server installed but hasnt configured the required environment variables
  • They ask about connecting to MongoDB/Atlas and dont have the credentials set up

Example prompts

  • “/mongodb-mcp-setup”

Requirements

  • Docker
  • A credential in MDB_MCP_API_CLIENT_SECRET
  • A credential in API_CLIENT_SECRET

Workflow steps

6 steps, taken from the step headings in SKILL.md.

  1. Detect Client
  2. Check Existing Configuration
  3. Present Configuration Options
  4. Determine Read-Only vs Read-Write Access
  5. Configure Credentials
  6. Next Steps

What it can do on your machine

Read from SKILL.md and the folder at commit 18b014e. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • docker

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • cloud.mongodb.com
    • mongodb.com
    • docker.com

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names these keys or tokens, usually read from environment variables:

    • MDB_MCP_API_CLIENT_SECRET
    • API_CLIENT_SECRET

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Mongodb MCP Setup loads about 3.3k tokens when it runs. Until then it costs about 73 tokens; SKILL.md has 1,531 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~73
When it runs · the whole SKILL.md, loaded when a task matches
~3.3k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from mongodb/agent-skills at commit 18b014e, republished under its Apache-2.0 licence (© mongodb). 1,531 words, ~3,310 tokens.

Download SKILL.mdSave it as .claude/skills/mongodb-mcp-setup/SKILL.md (or your agent's skills folder).
name
mongodb-mcp-setup
description
Guide users through configuring key MongoDB MCP server options. Use this skill when a user has the MongoDB MCP server installed but hasn't configured the required environment variables, or when they ask about connecting to MongoDB/Atlas and don't have the credentials set up.
license
Apache-2.0
metadata.version
1.0.0

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:

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

    • Quick setup for single cluster
    • Requires MDB_MCP_CONNECTION_STRING environment variable
  2. 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
  3. 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:

bash
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:

bash
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):

bash
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:

  1. Go to cloud.mongodb.com
  2. Select your cluster → click Connect
  3. Choose Drivers or Shell → copy the connection string
  4. 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:

  1. Navigate to MongoDB Atlas — cloud.mongodb.com
  2. Select your organization from the ORGANIZATION section near the top of the page
  3. Go to "Project Identity and Access" on the left sidebar → Applications → Create Service Account
  4. Set Permissions — Grant Organization Member or Project Owner (see docs for exact permission mappings)
  5. Generate Credentials — Create Client ID and Secret
    • ⚠️ The Client Secret is shown only once — save it immediately before leaving the page
  6. 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:

  1. On the service account details page, find API Access List
  2. Click Add Access List Entry
  3. 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.
  4. 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:

bash
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).

Show full SKILL.md (593 more words)Show less

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):

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

Codex (config.toml):

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

For Service Account (Option B):

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

bash
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):

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:

bash
# 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:

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

Codex:

bash
# 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):
  1. 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.
  2. Verify MCP Server: After restart, test by performing a MongoDB operation.

  3. 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):
  1. Ready to use: No restart or configuration needed!

  2. 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

© mongodb, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/mongodb-mcp-setup of mongodb/agent-skills.

Open the folder on GitHubat commit 18b014e

Used in 1 other repository

We found 3 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in mongodb/agent-skills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

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Categories

Questions about Mongodb MCP Setup

What does Mongodb MCP Setup do?

Guide users through configuring key MongoDB MCP server options. Mongodb MCP Setup is an agent skill from mongodb/agent-skills, published by the product's own GitHub organization. Guide users through configuring key MongoDB MCP server options.

When should I use Mongodb MCP Setup?

Mongodb MCP Setup fits situations like: A user has the MongoDB MCP server installed but hasnt configured the required environment variables; they ask about connecting to MongoDB/Atlas and dont have the credentials set up.

How do I install Mongodb MCP Setup in Claude Code?

Run `npx skills add mongodb/agent-skills --skill mongodb-mcp-setup -a claude-code`. Or copy the skill folder (skills/mongodb-mcp-setup in mongodb/agent-skills) into .claude/skills/mongodb-mcp-setup in your project. Claude Code loads it when a task matches its description.

How do I install Mongodb MCP Setup in Codex?

Run `npx skills add mongodb/agent-skills --skill mongodb-mcp-setup -a codex`. Or copy the skill folder (skills/mongodb-mcp-setup in mongodb/agent-skills) into .agents/skills/mongodb-mcp-setup in your project. Codex loads it when a task matches its description.

Can I use Mongodb MCP Setup in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add mongodb/agent-skills --skill mongodb-mcp-setup -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/mongodb-mcp-setup, .gemini/skills/mongodb-mcp-setup, .github/skills/mongodb-mcp-setup and .opencode/skills/mongodb-mcp-setup in your project.

What does Mongodb MCP Setup need to run?

Going by SKILL.md and its folder, Mongodb MCP Setup needs the command-line tools its instructions call (docker) and credentials named MDB_MCP_API_CLIENT_SECRET and API_CLIENT_SECRET. Our summary lists: Docker; A credential in MDB_MCP_API_CLIENT_SECRET; A credential in API_CLIENT_SECRET.

Does Mongodb MCP Setup access the network?

SKILL.md names 3 domains. As links in the text: cloud.mongodb.com, mongodb.com and docker.com. This is read from the text; nothing was executed.

Is Mongodb MCP Setup safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Mongodb MCP Setup use?

Mongodb MCP Setup is published under the Apache-2.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Mongodb MCP Setup use?

About 3.3k tokens (SKILL.md is roughly 13k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Mongodb MCP Setup?

Skills that share tags, products or a category with Mongodb MCP Setup: Mindsdb MCP Skill (LeoYeAI/openclaw-master-skills, 2.2k stars), Monstermq Broker Config (vogler75/monster-mq, 142 stars), Rhctl (saidake/rhctl, 106 stars) and Mongodb Replica Sets (TheDecipherist/claude-code-mastery-project-starter-kit, 338 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Mongodb MCP Setup?

mongodb (a GitHub organization, an official publisher) maintains it in mongodb/agent-skills, which has 190 GitHub stars. The repository holds 9 skills in this directory. The repository was last updated on October 6, 2026.

Source: mongodb/agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.