# How to integrate MongoDB MCP with Atomic Agent

```json
{
  "title": "How to integrate MongoDB MCP with Atomic Agent",
  "toolkit": "MongoDB MCP",
  "toolkit_slug": "mongodb_mcp",
  "framework": "Atomic Agent",
  "framework_slug": "atomic-agent",
  "url": "https://composio.dev/toolkits/mongodb_mcp/framework/atomic-agent",
  "markdown_url": "https://composio.dev/toolkits/mongodb_mcp/framework/atomic-agent.md",
  "updated_at": "2026-09-30T05:32:41.129Z"
}
```

## 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](https://atomicagent.io/docs/?cta_placement=atomic-agent-docs) for installation instructions.

## Also integrate MongoDB MCP with

- [ChatGPT](https://composio.dev/toolkits/mongodb_mcp/framework/chatgpt)
- [Claude Cowork](https://composio.dev/toolkits/mongodb_mcp/framework/claude-cowork)
- [Hermes](https://composio.dev/toolkits/mongodb_mcp/framework/hermes-agent)

## TL;DR

### 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 MCP to Atomic Agent

### Connect MongoDB to Atomic Agent
- Sign up or sign in to the [Composio dashboard](https://dashboard.composio.dev/?cta_placement=atomic-agent-api-key). 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.

## Supported Tools

| Tool slug | Name | Description |
|---|---|---|
| `MONGODB_MCP_AGGREGATE` | Aggregate | Run an aggregation against a MongoDB collection |
| `MONGODB_MCP_AGGREGATE_DB` | Aggregate-db | Run an aggregation against a MongoDB database |
| `MONGODB_MCP_ATLAS_CREATE_ACCESS_LIST` | Atlas-create-access-list | Allow Ip/CIDR ranges to access your MongoDB Atlas clusters. |
| `MONGODB_MCP_ATLAS_CREATE_CLUSTER` | Atlas-create-cluster | Create a MongoDB Atlas cluster (M10–M80, replica set or single shard, single or multi-region). Compute autoscaling is enabled by default: min instance size is set to the selected instance size, max is set two tiers above. Disk autoscaling is always enabled. For encryption at rest, the CMK provider must already have a valid configuration in the Atlas project. The tool returns immediately, use the atlas-inspect-cluster tool to poll the cluster state for readiness (state: IDLE). Connection strings are unavailable until the cluster reaches IDLE state. Note to LLM: Omit instance size unless specified by the user. If provider and regions are not already known, ask for both together in a single question before calling this tool. Common, non-exhaustive region default mappings by provider: AWS: "East Coast"/"Virginia"/"US East" → US_EAST_1, "Ohio" → US_EAST_2, "California"/"West Coast" → US_WEST_2, "Southeast Asia"/"APAC"/"Singapore" → AP_SOUTHEAST_1, "Europe"/"EU"/"Ireland" → EU_WEST_1. GCP: "Central US" → CENTRAL_US, "Western US" → WESTERN_US, "Southeast Asia"/"APAC" → SOUTHEASTERN_ASIA_PACIFIC, "Europe"/"EU" → WESTERN_EUROPE. AZURE: "East US" → US_EAST_2, "West US" → US_WEST_2, "Europe North" → EUROPE_NORTH, "Europe West" → EUROPE_WEST. Default recommendation: AWS US_EAST_1. User-specified regions not present in the mapping MUST be respected, rely on the tool to surface errors if a region is not supported. |
| `MONGODB_MCP_ATLAS_CREATE_DB_USER` | Atlas-create-db-user | Create an MongoDB Atlas database user |
| `MONGODB_MCP_ATLAS_CREATE_FREE_CLUSTER` | Atlas-create-free-cluster | Create a free MongoDB Atlas cluster |
| `MONGODB_MCP_ATLAS_CREATE_PROJECT` | Atlas-create-project | Create a MongoDB Atlas project |
| `MONGODB_MCP_ATLAS_GET_PERFORMANCE_ADVISOR` | 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 |
| `MONGODB_MCP_ATLAS_INSPECT_ACCESS_LIST` | Atlas-inspect-access-list | Inspect Ip/CIDR ranges with access to your MongoDB Atlas clusters. |
| `MONGODB_MCP_ATLAS_INSPECT_CLUSTER` | Atlas-inspect-cluster | Inspect metadata of a MongoDB Atlas cluster |
| `MONGODB_MCP_ATLAS_LIST_ALERTS` | Atlas-list-alerts | List triggered alerts for a MongoDB Atlas project. These are alerts Atlas has raised, not the alert configurations that define them. Defaults to OPEN alerts; set status to TRACKING or CLOSED to see others. |
| `MONGODB_MCP_ATLAS_LIST_CLUSTERS` | Atlas-list-clusters | List MongoDB Atlas clusters |
| `MONGODB_MCP_ATLAS_LIST_DB_USERS` | Atlas-list-db-users | List MongoDB Atlas database users |
| `MONGODB_MCP_ATLAS_LIST_ORGS` | Atlas-list-orgs | List MongoDB Atlas organizations |
| `MONGODB_MCP_ATLAS_LIST_PROJECTS` | Atlas-list-projects | List MongoDB Atlas projects. |
| `MONGODB_MCP_ATLAS_LOAD_SAMPLE_DATASET` | Atlas-load-sample-dataset | Load a MongoDB sample dataset into an Atlas cluster, or check the status of a previously-initiated load. To start a new load, provide `clusterName` — the load runs asynchronously and the response includes a `jobId` and initial state. To check progress, call this tool again with `jobId` (sample dataset loads typically take 1–5 minutes). State can be WORKING, COMPLETED, or FAILED. |
| `MONGODB_MCP_ATLAS_PAUSE_RESUME_CLUSTER` | Atlas-pause-resume-cluster | Pause or resume a dedicated (M10+) MongoDB Atlas cluster (Free and Flex clusters cannot be paused). Pause: paused clusters are unavailable for connections and do not incur compute costs. If the cluster being paused is the current active connection, it will be automatically disconnected. Returns an error if the cluster is already paused or not in a pausable state (must be IDLE). Resume: the cluster will not be immediately available after resuming. Use the atlas-inspect-cluster tool to poll the cluster state for readiness (state: IDLE). If the cluster is not paused, resuming it is a no-op. |
| `MONGODB_MCP_ATLAS_STREAMS_BUILD` | Atlas-streams-build | Create Atlas Stream Processing resources. Use this tool for 'set up a Kafka pipeline', 'create a workspace', 'add a connection', or 'deploy a processor'. Use resource='workspace' to create a new workspace (specify cloud provider, region, and tier). Use resource='connection' to add a data source or sink to an existing workspace. Use resource='processor' to deploy a stream processor with a pipeline. Use resource='privatelink' to set up private networking. Typical workflow: create workspace → add connections → deploy processor. |
| `MONGODB_MCP_ATLAS_STREAMS_DISCOVER` | Atlas-streams-discover | Discover and inspect Atlas Stream Processing resources. Also use for 'why is my processor failing', 'what workspaces do I have', 'show processor stats', or 'check processor health'. Use 'list-workspaces' to see all workspaces in a project. Use inspect actions for details on a specific resource. Use 'diagnose-processor' for a combined health report including state, stats, connection health, and recent errors. Use 'get-networking' for PrivateLink and account details. |
| `MONGODB_MCP_ATLAS_STREAMS_MANAGE` | Atlas-streams-manage | Manage Atlas Stream Processing resources: start/stop processors, modify pipelines, update configurations. Also use for 'change the pipeline', 'scale up my processor', or 'update my workspace tier'. Common workflow: action='stop-processor' → action='modify-processor' → action='start-processor'. Use `atlas-streams-discover` with action 'inspect-processor' to check state before managing. |
| `MONGODB_MCP_ATLAS_STREAMS_TEARDOWN` | Atlas-streams-teardown | Delete Atlas Stream Processing resources. Also use for 'remove my workspace', 'disconnect a source', 'delete all processors', or 'clean up my streams environment'. Performs basic safety checks before deletion: summarizes counts of processors and connections, highlights connections referenced by processors where possible, and surfaces API errors if processors are still running when deletion is attempted. Use `atlas-streams-discover` to review resources before deleting. |
| `MONGODB_MCP_ATLAS_UPGRADE_CLUSTER` | Atlas-upgrade-cluster | Upgrade a MongoDB Atlas cluster tier. Upgrades Free (M0) clusters to Flex or M10 Dedicated, or Flex clusters to M10 Dedicated. The upgrade path is determined automatically from the current tier unless overridden with targetTier. Note to LLM: If provider and region are not already known, ask for both together in a single question before calling this tool. Common region mappings by provider (default recommendation: AWS US_EAST_1): AWS: "East Coast"/"Virginia"/"US East" → US_EAST_1, "Ohio" → US_EAST_2, "California"/"West Coast" → US_WEST_2, "Southeast Asia"/"APAC"/"Singapore" → AP_SOUTHEAST_1, "Europe"/"EU"/"Ireland" → EU_WEST_1. GCP: "Central US" → CENTRAL_US, "Western US" → WESTERN_US, "Southeast Asia"/"APAC" → SOUTHEASTERN_ASIA_PACIFIC, "Europe"/"EU" → WESTERN_EUROPE. AZURE: "East US" → US_EAST_2, "West US" → US_WEST_2, "Europe"/"EU" → EUROPE_NORTH. |
| `MONGODB_MCP_COLLECTION_INDEXES` | Collection-indexes | Describe the indexes for a collection |
| `MONGODB_MCP_COLLECTION_SCHEMA` | Collection-schema | Describe the schema for a collection |
| `MONGODB_MCP_COLLECTION_STORAGE_SIZE` | Collection-storage-size | Gets the size of the collection |
| `MONGODB_MCP_COUNT` | Count | Gets the number of documents in a MongoDB collection using db.collection.count() and query as an optional filter parameter |
| `MONGODB_MCP_CREATE_COLLECTION` | Create-collection | Creates a new collection in a database. If the database doesn't exist, it will be created automatically. |
| `MONGODB_MCP_CREATE_INDEX` | Create-index | Create an index for a collection |
| `MONGODB_MCP_DB_STATS` | Db-stats | Returns statistics that reflect the use state of a single database |
| `MONGODB_MCP_DELETE_MANY` | Delete-many | Removes all documents that match the filter from a MongoDB collection |
| `MONGODB_MCP_DROP_COLLECTION` | Drop-collection | Removes a collection or view from the database. The method also removes any indexes associated with the dropped collection. |
| `MONGODB_MCP_DROP_DATABASE` | Drop-database | Removes the specified database, deleting the associated data files |
| `MONGODB_MCP_DROP_INDEX` | Drop-index | Drop an index for the provided database and collection. |
| `MONGODB_MCP_EXPLAIN` | Explain | Returns statistics describing the execution of the winning plan chosen by the query optimizer for the evaluated method |
| `MONGODB_MCP_FIND` | Find | Run a find query against a MongoDB collection |
| `MONGODB_MCP_INSERT_MANY` | Insert-many | Insert an array of documents into a MongoDB collection. If the list of documents is above com.mongodb/maxRequestPayloadBytes, consider inserting them in batches. |
| `MONGODB_MCP_LIST_COLLECTIONS` | List-collections | List all collections for a given database |
| `MONGODB_MCP_LIST_DATABASES` | List-databases | List all databases for a MongoDB connection |
| `MONGODB_MCP_REMOTE_ATLAS_CONNECT` | Remote-atlas-connect | Connect to MongoDB Atlas cluster |
| `MONGODB_MCP_RENAME_COLLECTION` | Rename-collection | Renames a collection in a MongoDB database |
| `MONGODB_MCP_UPDATE_MANY` | Update-many | Updates all documents that match the specified filter for a collection. If the list of documents is above com.mongodb/maxRequestPayloadBytes, consider updating them in batches. |

## Supported Triggers

None listed.

## 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](/pricing) for the current limits that apply to your connection.

## Complete Code

None listed.

## Conclusion

### 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](https://atomicagent.io/?cta_placement=atomic-agent-site) or inspect the [Atomic Agent source code](https://github.com/AtomicBot-ai/atomic-agent?cta_placement=atomic-agent-repo).

## How to build MongoDB MCP Agent with another framework

- [ChatGPT](https://composio.dev/toolkits/mongodb_mcp/framework/chatgpt)
- [Claude Cowork](https://composio.dev/toolkits/mongodb_mcp/framework/claude-cowork)
- [Hermes](https://composio.dev/toolkits/mongodb_mcp/framework/hermes-agent)

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## Frequently Asked Questions

### What are the differences in Tool Router MCP and MongoDB MCP?

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.

### Can I use Tool Router MCP with Atomic Agent?

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.

### Can I manage the permissions and scopes for MongoDB while using Tool Router?

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.

### How safe is my data with Composio Tool Router?

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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