Prevent MCP Tool Poisoning With a Registration Workflow

As organizations start to deploy AI agents in earnest, we are discovering just how easy it is to attack these kind of systems. I went into quite some detail about how “natural language” introduces new attack vectors in one of my recent blogs. These vulnerabilities aren’t merely theoretical. We’ve seen how a malicious Model Context Protocol (MCP) server could trick AI agents into leaking sensitive data like WhatsApp chat histories and SSH keys without user awareness. An Agent Mesh lays a secure network foundation, but for that to work, we need to consider fundamentals of registration and attestation.

The fundamental problem stems from a lack of centralized governance and verification mechanisms. Currently, when an AI agent connects to an MCP server or another agent via Agent-to-Agent (A2A), there’s no standardized way to verify the server’s legitimacy or ensure tools haven’t been maliciously modified after initial usage. A lot of these attacks could be prevented with a combination of registration workflows and runtime data-plane enforcement. In this blog, we’ll go into how that could look and work in practice.

The Secure Agent Architecture: Registration Catalog and Agent Gateway

A comprehensive security architecture for AI agent ecosystems in an enterprise requires two complementary components working in tandem:

1. Registration Catalog - Enforces registration workflows, maintains verified identities, cryptographic signatures, and security attestations
2. Agent Gateway - Acts as a secure intermediary that enforces verification against the catalog

This architecture creates a defense-in-depth approach where multiple security layers protect against various attack vectors. Let’s explore how this works in practice.

Registration Workflow in Action

Let’s explore how a robust registration workflow integrated with an agent gateway might work through a hypothetical example:

Example: Enterprise Agent Registration

Imagine a well-known global financial institution has implemented a comprehensive agentic security system around MCP and A2A. Here’s how their workflow operates:

Step 1: Developer Registration
Before submitting any tools or agents, developers complete a thorough verification process. Only approved developers can submit new MCP servers, A2A agents, or make changes:

Developer: Jane Smith requests account on `AI Agent Portal`AI 
Agent Portal: Validates Jane's identity through:
- Corporate email verification
- Two-factor authentication setup
- Digital signature creation (using PKI infrastructure)
- Acceptance of code of conduct and security policies

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Step 2: Tool/Agent Submission
When Jane develops a new MCP server for generating financial reports, she submits it through the portal:

Submission includes:
- Source code repository link, git commits, etc
- Requested names and versions for MCP server / A2A 
- Tool description (visible to both humans and AI)
- Requested permissions and access scopes
- Dependencies and third-party components
- Comprehensive documentation

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Step 3: Security Scanning
The registration portal performs multiple automated analyses:

Security scans performed:
- Search for name collisions or similarities
- Dynamic testing in sandboxed environment
- Tool description parsing for potential poisoning attempts
- Dependency vulnerability scanning
- Semantic analysis of instructions to detect manipulation / shadow attacks

Take a look at this video to see how automated security could be implemented in an agent-registration workflow:

Step 4: Human Review
For tools requesting elevated permissions (such as access to customer financial data, payment processing APIs, trade execution APIs, etc), a security team performs additional review:

Security team actions:
- Reviews scan results
- Tests tool functionality against stated purpose
- Verifies permission requests match functionality
- Checks for overly broad data access
- Evaluates privacy implications

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Step 5: Digital Signing and Catalog Entry
Upon approval, the portal then:

- Assigns a namespace, or approved name for MCP server, tools, or agents
- Generates a cryptographic signature for each tool and its description
- Generates a Certificate for this MCP Server or A2A agent
- Stores the approved signatures, certificates, versions, and descriptions in an immutable registry
- Creates a catalog entry which can be searched and consumed
- Logs all approval details for auditing

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The Agent Gateway: Enforcement

The agent gateway isn’t merely a simple proxy—it’s an intelligent security enforcement point for the entire MCP/A2A ecosystem. It forms the foundation of a Agent Mesh. Its capabilities include:

1. Signature Verification

When an MCP client requests a list of tools from a server (or an agent requests an A2A AgentCard), the gateway acts as a security checkpoint:

The gateway intercepts the tool descriptions returned by the MCP server and compares their cryptographic signatures against those stored in the trusted registration catalog. Any discrepancies, potentially indicating a tool poisoning attempt or a rug pull, result in the tool being filtered out or flagged.

2. Tool Description Sanitization

Even with verified tools, the gateway can enforce additional security:

For each tool description:
- Remove potentially harmful directives
- Apply sanitization rules
- Normalize formatting
- Enforce length limitations
- Filter out excessive privilege requests

This provides an additional layer of protection against tool descriptions that might contain subtle manipulation attempts.

3. Access Control Enforcement

The gateway integrates with enterprise identity systems to enforce fine-grained access:

When processing tool invocation:
- Verify user/agent identity
- Check authorization for specific tool
- Apply contextual access policies
- Enforce data handling restrictions
- Log access for compliance purposes

4. Centralized Audit Trail

By positioning the agent gateway as a mandatory intermediary, organizations gain comprehensive visibility:

Gateway logging includes:
- All tool discovery requests
- Tool invocations with parameters
- Verification results
- Access decisions
- Response data (with appropriate privacy controls)

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This centralized logging is invaluable for security monitoring, compliance reporting, and incident response.

Agent Registration Workflows: Best Practices

1. Integrate with existing security infrastructure. Leverage your current IAM, PKI, and security monitoring systems rather than building everything from scratch. Be sensitive to protocols (MCP, A2A) that try to specify too much in the protocol; leverage transport security
   
   
2. Design for scale from the beginning. Expect that you’ll be running a lot of AI agents; plan for a secure foundation vs treating everything as a PoC that takes bad habits to production
   
   
3. Implement progressive verification. Apply more rigorous checks to high-risk tools and operations while using lighter verification for low-risk activities.
   
   
4. Make security transparent to users. While verification happens behind the scenes, provide clear indicators of tool verification status to both end-users and AI agents.
   
   
5. Plan for ecosystem expansion. Design your architecture to eventually support cross-organizational trust and verification as your AI agents begin to interact with external systems.
   
   

A Secure Foundation for AI Agent Ecosystems

The combination of a robust registration workflow, a comprehensive catalog, and secure agent gateways provides the foundation for trustworthy AI agent ecosystems. This Agent Mesh architecture directly addresses the critical vulnerabilities researchers have identified in MCP and A2A implementations.

By verifying tool authenticity, enforcing access controls, and maintaining a secure chain of trust between development and execution, organizations can confidently deploy powerful AI agent capabilities while protecting against sophisticated attacks.

As AI agents become increasingly autonomous and integrated into critical business processes, this security architecture will be essential for responsible deployment at scale. The investment in building these security foundations today will pay dividends as AI agent capabilities continue to expand in the future. Read more about this Agent Mesh architecture in detail, and reach out if you have questions.

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