How to integrate Pinecone MCP with Claude Agent SDK

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Introduction

This guide walks you through connecting Pinecone to the Claude Agent SDK using the Composio tool router. By the end, you'll have a working Pinecone agent that can query all vectors similar to user question, upsert document embeddings into a namespace, delete vectors from the archive index through natural language commands.

This guide will help you understand how to give your Claude Agent SDK agent real control over a Pinecone account through Composio's Pinecone MCP server.

Before we dive in, let's take a quick look at the key ideas and tools involved.

TL;DR

Here's what you'll learn:
  • Get and set up your Claude/Anthropic and Composio API keys
  • Install the necessary dependencies
  • Initialize Composio and create a Tool Router session for Pinecone
  • Configure an AI agent that can use Pinecone as a tool
  • Run a live chat session where you can ask the agent to perform Pinecone operations

What is Claude Agent SDK?

The Claude Agent SDK is Anthropic's official framework for building AI agents powered by Claude. It provides a streamlined interface for creating agents with MCP tool support and conversation management.

Key features include:

  • Native MCP Support: Built-in support for Model Context Protocol servers
  • Permission Modes: Control tool execution permissions
  • Streaming Responses: Real-time response streaming for interactive applications
  • Context Manager: Clean async context management for sessions

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.

Supported Tools & Triggers

Tools
Cancel Bulk ImportTool to cancel a bulk import operation in Pinecone.
Configure IndexTool to configure an existing Pinecone index, including pod type, replicas, deletion protection, and tags.
Create BackupTool to create a backup of a Pinecone index for disaster recovery and version control.
Create IndexTool to create a Pinecone index with specified configuration.
Create Index with Embedding ModelTool to create a Pinecone index with integrated embedding model for automatic vectorization.
Create Index from BackupTool to create an index from a backup.
Create NamespaceTool to create a namespace within a serverless Pinecone index.
Delete IndexTool to permanently delete a Pinecone index.
Delete NamespaceTool to permanently delete a namespace from a serverless index.
Describe BackupTool to retrieve detailed information about a specific backup.
Describe Bulk ImportTool to describe a specific bulk import operation in Pinecone.
Describe Index StatsTool to get index statistics including vector count per namespace, dimensions, and fullness.
Describe Restore JobTool to get detailed information about a specific restore job in Pinecone.
Generate EmbeddingsTool to generate vector embeddings for input text using Pinecone's hosted embedding models.
Get Model InformationTool to retrieve detailed information about a specific model hosted by Pinecone.
List Bulk ImportsTool to list all recent and ongoing bulk import operations in Pinecone.
List CollectionsTool to list all collections in a Pinecone project (pod-based indexes only).
List Index BackupsTool to list all backups for a specific Pinecone index.
List IndexesTool to list all indexes in a Pinecone project.
List Available ModelsTool to list all available embedding and reranking models hosted by Pinecone.
List NamespacesTool to list all namespaces in a serverless Pinecone index.
List Project BackupsTool to list all backups for indexes in a Pinecone project.
List Restore JobsTool to list all restore jobs for a project with pagination support.
List VectorsTool to list vector IDs in a Pinecone serverless index.
Query VectorsTool to perform semantic search within a Pinecone index using a query vector.
Rerank DocumentsTool to rerank documents by semantic relevance to a query.
Search Records in NamespaceTool to search records within a Pinecone namespace using text, vector, or ID query.
Start Bulk ImportTool to start an asynchronous bulk import of vectors from object storage (S3, GCS, or Azure Blob Storage) into a Pinecone index.
Update VectorTool to update a vector in Pinecone by ID.
Upsert Records to NamespaceTool to upsert text records into a Pinecone namespace.

What is the Composio tool router, and how does it fit here?

What is Tool Router?

Composio's Tool Router helps agents find the right tools for a task at runtime. You can plug in multiple toolkits (like Gmail, HubSpot, and GitHub), and the agent will identify the relevant app and action to complete multi-step workflows. This can reduce token usage and improve the reliability of tool calls. Read more here: Getting started with Tool Router

The tool router generates a secure MCP URL that your agents can access to perform actions.

How the Tool Router works

The Tool Router follows a three-phase workflow:

  1. Discovery: Searches for tools matching your task and returns relevant toolkits with their details.
  2. Authentication: Checks for active connections. If missing, creates an auth config and returns a connection URL via Auth Link.
  3. Execution: Executes the action using the authenticated connection.

Step-by-step Guide

Prerequisites

Before starting, make sure you have:
  • Composio API Key and Claude/Anthropic API Key
  • Primary know-how of Claude Agents SDK
  • A Pinecone account
  • Some knowledge of Python

Getting API Keys for Claude/Anthropic and Composio

Claude/Anthropic API Key
  • Go to the Anthropic Console and create an API key. You'll need credits to use the models.
  • Keep the API key safe.
Composio API Key
  • Log in to the Composio dashboard.
  • Navigate to your API settings and generate a new API key.
  • Store this key securely as you'll need it for authentication.

Install dependencies

pip install composio-anthropic claude-agent-sdk python-dotenv

Install the Composio SDK and the Claude Agents SDK.

What's happening:

  • composio-anthropic provides Composio integration for Anthropic
  • claude-agent-sdk is the core agent framework
  • python-dotenv loads environment variables

Set up environment variables

bash
COMPOSIO_API_KEY=your_composio_api_key_here
USER_ID=your_user_id_here
ANTHROPIC_API_KEY=your_anthropic_api_key_here

Create a .env file in your project root.

What's happening:

  • COMPOSIO_API_KEY authenticates with Composio
  • USER_ID identifies the user for session management
  • ANTHROPIC_API_KEY authenticates with Anthropic/Claude

Import dependencies

import asyncio
from claude_agent_sdk import ClaudeSDKClient, ClaudeAgentOptions
import os
from composio import Composio
from dotenv import load_dotenv

load_dotenv()
What's happening:
  • We're importing all necessary libraries including the Claude Agent SDK and Composio
  • The load_dotenv() function loads environment variables from your .env file
  • This setup prepares the foundation for connecting Claude with Pinecone functionality

Create a Composio instance and Tool Router session

async def chat_with_remote_mcp():
    api_key = os.getenv("COMPOSIO_API_KEY")
    if not api_key:
        raise RuntimeError("COMPOSIO_API_KEY is not set")

    composio = Composio(api_key=api_key)

    # Create Tool Router session for Pinecone
    mcp_server = composio.create(
        user_id=os.getenv("USER_ID"),
        toolkits=["pinecone"]
    )

    url = mcp_server.mcp.url

    if not url:
        raise ValueError("Session URL not found")
What's happening:
  • The function checks for the required COMPOSIO_API_KEY environment variable
  • We're creating a Composio instance using our API key
  • The create method creates a Tool Router session for Pinecone
  • The returned url is the MCP server URL that your agent will use

Configure Claude Agent with MCP

# Configure remote MCP server for Claude
options = ClaudeAgentOptions(
    permission_mode="bypassPermissions",
    mcp_servers={
        "composio": {
            "type": "http",
            "url": url,
            "headers": {
                "x-api-key": os.getenv("COMPOSIO_API_KEY")
            }
        }
    },
    system_prompt="You are a helpful assistant with access to Pinecone tools via Composio.",
    max_turns=10
)
What's happening:
  • We're configuring the Claude Agent options with the MCP server URL
  • permission_mode="bypassPermissions" allows the agent to execute operations without asking for permission each time
  • The system prompt instructs the agent that it has access to Pinecone
  • max_turns=10 limits the conversation length to prevent excessive API usage

Create client and start chat loop

# Create client with context manager
async with ClaudeSDKClient(options=options) as client:
    print("\nChat started. Type 'exit' or 'quit' to end.\n")

    # Main chat loop
    while True:
        user_input = input("You: ").strip()
        if user_input.lower() in {"exit", "quit"}:
            print("Goodbye!")
            break

        # Send query
        await client.query(user_input)

        # Receive and print response
        print("Claude: ", end="", flush=True)
        async for message in client.receive_response():
            if hasattr(message, "content"):
                for block in message.content:
                    if hasattr(block, "text"):
                        print(block.text, end="", flush=True)
        print()
What's happening:
  • The Claude SDK client is created using the async context manager pattern
  • The agent processes each query and streams the response back in real-time
  • The chat loop continues until the user types 'exit' or 'quit'

Run the application

if __name__ == "__main__":
    asyncio.run(chat_with_remote_mcp())
What's happening:
  • This entry point runs the async chat_with_remote_mcp() function using asyncio.run()
  • The application will start, create the MCP connection, and begin the interactive chat session

Complete Code

Here's the complete code to get you started with Pinecone and Claude Agent SDK:

import asyncio
from claude_agent_sdk import ClaudeSDKClient, ClaudeAgentOptions
import os
from composio import Composio
from dotenv import load_dotenv

load_dotenv()

async def chat_with_remote_mcp():
    api_key = os.getenv("COMPOSIO_API_KEY")
    if not api_key:
        raise RuntimeError("COMPOSIO_API_KEY is not set")

    composio = Composio(api_key=api_key)

    # Create Tool Router session for Pinecone
    mcp_server = composio.create(
        user_id=os.getenv("USER_ID"),
        toolkits=["pinecone"]
    )

    url = mcp_server.mcp.url

    if not url:
        raise ValueError("Session URL not found")

    # Configure remote MCP server for Claude
    options = ClaudeAgentOptions(
        permission_mode="bypassPermissions",
        mcp_servers={
            "composio": {
                "type": "http",
                "url": url,
                "headers": {
                    "x-api-key": os.getenv("COMPOSIO_API_KEY")
                }
            }
        },
        system_prompt="You are a helpful assistant with access to Pinecone tools via Composio.",
        max_turns=10
    )

    # Create client with context manager
    async with ClaudeSDKClient(options=options) as client:
        print("\nChat started. Type 'exit' or 'quit' to end.\n")

        # Main chat loop
        while True:
            user_input = input("You: ").strip()
            if user_input.lower() in {"exit", "quit"}:
                print("Goodbye!")
                break

            # Send query
            await client.query(user_input)

            # Receive and print response
            print("Claude: ", end="", flush=True)
            async for message in client.receive_response():
                if hasattr(message, "content"):
                    for block in message.content:
                        if hasattr(block, "text"):
                            print(block.text, end="", flush=True)
            print()

if __name__ == "__main__":
    asyncio.run(chat_with_remote_mcp())

Conclusion

You've successfully built a Claude Agent SDK agent that can interact with Pinecone through Composio's Tool Router.

Key features:

  • Native MCP support through Claude's agent framework
  • Streaming responses for real-time interaction
  • Permission bypass for smooth automated workflows
You can extend this by adding more toolkits, implementing custom business logic, or building a web interface around the agent.

How to build Pinecone MCP Agent with another framework

OpenAI Agents SDK

OpenAI Agents SDK

Use Pinecone MCP with OpenAI Agents SDK

Google ADK

Google ADK

Use Pinecone MCP with Google ADK

LangChain

LangChain

Use Pinecone MCP with LangChain

Vercel AI SDK

Vercel AI SDK

Use Pinecone MCP with Vercel AI SDK

Mastra AI

Mastra AI

Use Pinecone MCP with Mastra AI

LlamaIndex

LlamaIndex

Use Pinecone MCP with LlamaIndex

CrewAI

CrewAI

Use Pinecone MCP with CrewAI

Claude Code

Claude Code

Use Pinecone MCP with Claude Code

Codex

Codex

Use Pinecone MCP with Codex

FAQ

What are the differences in Tool Router MCP and Pinecone MCP?

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.

Can I use Tool Router MCP with Claude Agent SDK?

Yes, you can. Claude Agent SDK 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.

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

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.

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 Pinecone data and credentials are handled as safely as possible.

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