How to integrate Pinecone MCP with Atomic Agent

Connect Atomic Agent to Pinecone MCP. Query all vectors similar to user question, upsert document embeddings into a namespace, and more using natural language, with authentication handled for you.

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Pinecone is a fully managed vector database for high-performance AI memory and search. It lets you scale semantic search and retrieval without infrastructure overhead.

30 Tools

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 Pinecone.

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 Pinecone account. See the Atomic Agent documentation for installation instructions.

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How Atomic Agent connects to Pinecone

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 Pinecone to Atomic Agent

  1. Sign up or sign in to the Composio dashboard. Copy your API key.
  2. 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.
  3. Ask Atomic Agent to do something in Pinecone. It searches Composio for the right tool.
  4. On first use, open the sign-in link returned in the chat. Connect your Pinecone 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 Pinecone MCP server, and what's possible with it?

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

Use Pinecone from Atomic Agent

With your account connected, ask Atomic Agent to work with Pinecone 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 Pinecone action and event your agent gets out of the box.

Cancel Bulk Import

Tool to cancel a bulk import operation in Pinecone.

Configure Index

Tool to configure an existing Pinecone index, including pod type, replicas, deletion protection, and tags.

Create Backup

Tool to create a backup of a Pinecone index for disaster recovery and version control.

Create Index

Tool to create a Pinecone index with specified configuration.

Create Index with Embedding Model

Tool to create a Pinecone index with integrated embedding model for automatic vectorization.

Create Index from Backup

Tool to create an index from a backup.

Create Namespace

Tool to create a namespace within a serverless Pinecone index.

Delete Index

Tool to permanently delete a Pinecone index.

Delete Namespace

Tool to permanently delete a namespace from a serverless index.

Describe Backup

Tool to retrieve detailed information about a specific backup.

Describe Bulk Import

Tool to describe a specific bulk import operation in Pinecone.

Describe Index Stats

Tool to get index statistics including vector count per namespace, dimensions, and fullness.

Describe Restore Job

Tool to get detailed information about a specific restore job in Pinecone.

Generate Embeddings

Tool to generate vector embeddings for input text using Pinecone's hosted embedding models.

Get Model Information

Tool to retrieve detailed information about a specific model hosted by Pinecone.

List Bulk Imports

Tool to list all recent and ongoing bulk import operations in Pinecone.

List Collections

Tool to list all collections in a Pinecone project (pod-based indexes only).

List Index Backups

Tool to list all backups for a specific Pinecone index.

List Indexes

Tool to list all indexes in a Pinecone project.

List Available Models

Tool to list all available embedding and reranking models hosted by Pinecone.

List Namespaces

Tool to list all namespaces in a serverless Pinecone index.

List Project Backups

Tool to list all backups for indexes in a Pinecone project.

List Restore Jobs

Tool to list all restore jobs for a project with pagination support.

List Vectors

Tool to list vector IDs in a Pinecone serverless index.

Query Vectors

Tool to perform semantic search within a Pinecone index using a query vector.

Rerank Documents

Tool to rerank documents by semantic relevance to a query.

Search Records in Namespace

Tool to search records within a Pinecone namespace using text, vector, or ID query.

Start Bulk Import

Tool to start an asynchronous bulk import of vectors from object storage (S3, GCS, or Azure Blob Storage) into a Pinecone index.

Update Vector

Tool to update a vector in Pinecone by ID.

Upsert Records to Namespace

Tool to upsert text records into a Pinecone namespace.

FAQ

Frequently asked questions

With a standalone Pinecone MCP server, the agents and LLMs can only access a fixed set of Pinecone tools tied to that server. However, with the Composio Tool Router, agents can dynamically load tools from Pinecone 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 Pinecone tools.

Yes, absolutely. You can configure which Pinecone 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 Pinecone data and credentials are handled as safely as possible.

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