How to integrate MongoDB MCP with Atomic Agent

Connect Atomic Agent to MongoDB MCP. List collections in your production database, query top slow queries from cluster, and more using natural language, with authentication handled for you.

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MongoDB MCP

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MongoDB MCP is MongoDB's managed interface for accessing Atlas resources and data. Use it for secure, centralized access to clusters, databases, and collections.

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Introduction

Atomic Agent is an open-source AI agent that runs on your machine and supports local models through llama.cpp. Connect it to 1,500+ apps through Composio, including MongoDB.

This guide uses Atomic Agent's built-in Composio integration. You need Atomic Agent v0.5.6 or later, your own Composio API key, and a MongoDB account. See the Atomic Agent documentation for installation instructions.

Also integrate MongoDB MCP with

ChatGPT Claude Cowork Hermes

How Atomic Agent connects to MongoDB

Atomic Agent connects to Composio's Tool Router over Streamable HTTP MCP. It discovers the tools needed for your request, and Composio handles account authentication.

Execution and account-connection tools follow Atomic Agent's configured approval policy. Review any approval prompt before allowing an action on your connected account.

Connect MongoDB to Atomic Agent

Sign up or sign in to the Composio dashboard. Copy your API key.
In Atomic Agent, open the Integrations tab and select Composio. Select API key, press e, paste the key, and press Enter. The tools become available immediately, without a restart.
Ask Atomic Agent to do something in MongoDB. It searches Composio for the right tool.
On first use, open the sign-in link returned in the chat. Connect your MongoDB account, then return to Atomic Agent to continue.

Headless setup

Add the following line to ~/.atomic-agent/.env, replacing YOUR_COMPOSIO_API_KEY with your key. Start Atomic Agent after saving the file.

bash

COMPOSIO_API_KEY=YOUR_COMPOSIO_API_KEY

What is the MongoDB MCP server, and what's possible with it?

The MongoDB MCP server is an implementation of the Model Context Protocol that connects your AI agent and assistants like Claude, Cursor, etc directly to your MongoDB account. It provides structured and secure access so your agent can perform MongoDB operations on your behalf.

Use MongoDB from Atomic Agent

With your account connected, ask Atomic Agent to work with MongoDB in natural language. You can connect more apps through the same Composio integration as you need them.

Visit the Atomic Agent website or inspect the Atomic Agent source code.

Troubleshooting

Why is my API key rejected?

Copy the key directly from the Composio dashboard. Atomic Agent requires ASCII characters because it sends the key in an HTTP header. Remove any extra characters introduced when copying.

Why are Composio tools unavailable after saving a key?

Check that you use Atomic Agent v0.5.6 or later and that Composio is enabled in your configuration. A "composio": { "enabled": false } setting disables the integration while keeping the saved key on disk.

Does Composio have a free plan?

The Hobby plan includes 100,000 tool calls per month. Composio-managed OAuth apps have a lower included allowance. See Composio pricing for the current limits that apply to your connection.

TOOLS

Supported Tools

Every MongoDB MCP action and event your agent gets out of the box.

Aggregate

Run an aggregation against a MongoDB collection

Aggregate-db

Run an aggregation against a MongoDB database

Atlas-create-access-list

Allow Ip/CIDR ranges to access your MongoDB Atlas clusters.

Atlas-create-cluster

Create a MongoDB Atlas cluster (M10–M80, replica set or single shard, single or multi-region).

Atlas-create-db-user

Create an MongoDB Atlas database user

Atlas-create-free-cluster

Create a free MongoDB Atlas cluster

Atlas-create-project

Create a MongoDB Atlas project

Atlas-get-performance-advisor

Get MongoDB Atlas performance advisor recommendations and suggestions, which includes the operations: suggested indexes, drop index suggestions, schema suggestions, and a sample of the most recent (max 50) slow query logs

Atlas-inspect-access-list

Inspect Ip/CIDR ranges with access to your MongoDB Atlas clusters.

Atlas-inspect-cluster

Inspect metadata of a MongoDB Atlas cluster

Atlas-list-alerts

List triggered alerts for a MongoDB Atlas project.

Atlas-list-clusters

List MongoDB Atlas clusters

Atlas-list-db-users

List MongoDB Atlas database users

Atlas-list-orgs

List MongoDB Atlas organizations

Atlas-list-projects

List MongoDB Atlas projects.

Atlas-load-sample-dataset

Load a MongoDB sample dataset into an Atlas cluster, or check the status of a previously-initiated load.

Atlas-pause-resume-cluster

Pause or resume a dedicated (M10+) MongoDB Atlas cluster (Free and Flex clusters cannot be paused).

Atlas-streams-build

Create Atlas Stream Processing resources.

Atlas-streams-discover

Discover and inspect Atlas Stream Processing resources.

Atlas-streams-manage

Manage Atlas Stream Processing resources: start/stop processors, modify pipelines, update configurations.

Atlas-streams-teardown

Delete Atlas Stream Processing resources.

Atlas-upgrade-cluster

Upgrade a MongoDB Atlas cluster tier.

Collection-indexes

Describe the indexes for a collection

Collection-schema

Describe the schema for a collection

Collection-storage-size

Gets the size of the collection

Count

Gets the number of documents in a MongoDB collection using db.

Create-collection

Creates a new collection in a database.

Create-index

Create an index for a collection

Db-stats

Returns statistics that reflect the use state of a single database

Delete-many

Removes all documents that match the filter from a MongoDB collection

Drop-collection

Removes a collection or view from the database.

Drop-database

Removes the specified database, deleting the associated data files

Drop-index

Drop an index for the provided database and collection.

Explain

Returns statistics describing the execution of the winning plan chosen by the query optimizer for the evaluated method

Find

Run a find query against a MongoDB collection

Insert-many

Insert an array of documents into a MongoDB collection.

List-collections

List all collections for a given database

List-databases

List all databases for a MongoDB connection

Remote-atlas-connect

Connect to MongoDB Atlas cluster

Rename-collection

Renames a collection in a MongoDB database

Update-many

Updates all documents that match the specified filter for a collection.

FRAMEWORKS

How to build MongoDB MCP Agent with another framework

ChatGPT

Use MongoDB MCP with ChatGPT

Claude Cowork

Use MongoDB MCP with Claude Cowork

Hermes

Use MongoDB MCP with Hermes

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FAQ

Frequently asked questions

With a standalone MongoDB MCP server, the agents and LLMs can only access a fixed set of MongoDB tools tied to that server. However, with the Composio Tool Router, agents can dynamically load tools from MongoDB and many other apps based on the task at hand, all through a single MCP endpoint.

Yes, you can. Atomic Agent fully supports MCP integration. You get structured tool calling, message history handling, and model orchestration while Tool Router takes care of discovering and serving the right MongoDB tools.

Yes, absolutely. You can configure which MongoDB scopes and actions are allowed when connecting your account to Composio. You can also bring your own OAuth credentials or API configuration so you keep full control over what the agent can do.

All sensitive data such as tokens, keys, and configuration is fully encrypted at rest and in transit. Composio is SOC 2 Type 2 compliant and follows strict security practices so your MongoDB data and credentials are handled as safely as possible.

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