MCP security considerations for enterprise deployments

[aarora79]

MCP Security Considerations for Enterprise Gateway and Registry Deployments

Overview

This discussion examines security considerations for onboarding new MCP servers into the MCP Gateway and Registry project, particularly in enterprise environments where hundreds of MCP servers may be deployed across different teams. While the gateway implements authentication and authorization mechanisms (OAuth 2.0 PKCE flow, Amazon Cognito integration), this analysis addresses broader security aspects essential for production deployments, especially when onboarding MCP servers from untrusted sources (such as public MCP servers in enterprise environments) or when organizations cannot rely solely on individual developers to ensure MCP server security.

For the latest MCP protocol security guidelines, refer to the MCP Security Best Practices and Authorization specifications.

Enterprise Deployment Context

In typical enterprise environments, we expect:

• Hundreds of MCP servers created by different teams with varying security expertise
• Rapid deployment cycles as teams adopt MCP for various use cases
• Complex supply chains when enterprises package MCP gateways as products
• Regulatory compliance requirements (SOC2, ISO 27001, GDPR, HIPAA)
• Multi-tenancy requirements serving multiple business units or external customers

These characteristics mirror challenges seen in microservices architectures and API gateway deployments, requiring established enterprise security practices adapted for MCP's specific protocol features.

Security Risk Analysis

Based on analysis of multiple security resources and enterprise deployment considerations:

1. Supply Chain Security

Supply chain attacks represent a significant risk in distributed systems. For MCP deployments, specific concerns include:

Risk Factors:

• Dependency confusion attacks when MCP servers use public package registries
• Typosquatting risks with similarly named malicious servers
• Time-of-check vs time-of-use vulnerabilities during security scanning
• Transitive dependency vulnerabilities
• Build pipeline compromise risks

Mitigation Strategies:

While it may not be practical to implement all of these security measures directly in the gateway at onboarding time, one approach could require administrators or developers to provide proof of having run these security tools before onboarding their MCP server. This could take the form of reports generated by these tools, which can then be automatically examined by an LLM as part of the MCP server onboarding workflow. The LLM could provide automated decisions (approve/reject) or flag cases requiring human review when the security posture is unclear. This approach balances freedom and responsibility with automated verification and trust.

For source code analysis, language-specific tools should be employed:

• Python: Bandit for SAST, pip-audit for dependency scanning, safety for vulnerability database checks
• JavaScript/TypeScript: Snyk or npm audit for dependencies, ESLint with security plugins, Semgrep for pattern-based analysis
• Go: Nancy for dependency scanning, gosec for security linting, go-mod-outdated for version management
• Java: SpotBugs with Find Security Bugs, OWASP Dependency Check

For containerized deployments:

• Trivy or Grype for vulnerability scanning
• Cosign for container signing and verification
• SLSA compliance for build provenance
• in-toto for supply chain attestations

For runtime security:

• Falco for behavioral monitoring
• eBPF-based tools for system call monitoring
• Network policy enforcement
• Resource usage monitoring

2. Command Execution Controls

MCP servers that execute commands require careful security controls, similar to those used in CI/CD systems and remote execution frameworks.

Common Attack Patterns:

• Path traversal through manipulated file paths
• Command injection via unsanitized parameters
• Resource exhaustion attacks
• Privilege escalation attempts

Defense Strategies:

Implement a security middleware layer:

┌─────────────────┐     ┌──────────────────┐     ┌─────────────────┐
│   MCP Client    │────▶│ Security Gateway │────▶│   MCP Server    │
└─────────────────┘     └──────────────────┘     └─────────────────┘
                               │
                               ▼
                        ┌──────────────┐
                        │ Policy Engine│
                        ├──────────────┤
                        │ • Input Valid │
                        │ • Rate Limits│
                        │ • Sandboxing │
                        └──────────────┘

Key controls include:

• Input validation using schema enforcement
• Parameter sanitization following OWASP guidelines
• Command allowlisting rather than denylisting
• Execution within sandboxed environments (containers, VMs)
• Resource quotas and timeouts

3. Prompt Injection Prevention

Prompt injection represents an AI-specific security challenge requiring specialized defenses beyond traditional input validation.

Defense Layers:

1. Input Processing: Sanitize control characters, enforce length limits
2. Semantic Analysis: Deploy specialized models to detect injection attempts
3. Output Validation: Verify responses match expected patterns
4. Context Separation: Maintain clear boundaries between system and user prompts
5. Detection Mechanisms: Implement canary tokens to identify data leakage

These approaches parallel SQL injection prevention but require AI-specific adaptations.

4. Tool Discovery and Injection Prevention

MCP's dynamic tool discovery mechanism requires security controls similar to plugin architectures in other systems.

Security Measures:

• Cryptographic signing of tool definitions
• Behavioral monitoring comparing declared vs actual functionality
• Reputation scoring based on usage patterns and community feedback
• Graduated permission models where tools earn trust over time
• Mandatory security metadata in tool manifests

5. Authentication and Authorization Challenges

The confused deputy problem and token management issues are well-known in distributed systems:

Token Management Best Practices:

• Implement token scoping with explicit audience claims
• Use mutual TLS for service-to-service communication
• Deploy request signing (HMAC, JWT) to prevent tampering
• Maintain comprehensive audit trails for compliance
• Implement token rotation and revocation mechanisms

6. Session Security

Session management in MCP deployments should follow established web application security practices:

• Bind sessions to client characteristics (IP, device fingerprint)
• Implement adaptive timeout policies based on risk levels
• Support immediate revocation on anomaly detection
• Encrypt session data at rest using hardware security modules
• Regular session cleanup and rotation

7. Compliance and Data Governance

Enterprise deployments must address regulatory requirements:

GDPR Considerations:

• Data retention policies for MCP interaction logs
• User data export capabilities for portability requirements
• Right to erasure implementation across distributed logs
• Privacy by design in tool development

SOC2 and ISO 27001 Requirements:

• Change management processes for MCP server updates
• Access control reviews and certification
• Encryption standards for data in transit and at rest
• Incident response procedures
• Business continuity planning

8. Multi-Tenancy Architecture

Enterprise MCP gateways must provide strong isolation between tenants:

┌──────────────────────────────────────────┐
│          MCP Gateway (Multi-tenant)       │
├────────────┬────────────┬────────────────┤
│  Tenant A  │  Tenant B  │    Tenant C    │
├────────────┼────────────┼────────────────┤
│ • Isolated │ • Isolated │ • Isolated     │
│ • Quotas   │ • Quotas   │ • Quotas       │
│ • Encrypted│ • Encrypted│ • Encrypted    │
└────────────┴────────────┴────────────────┘

Implementation considerations:

• Network isolation using segmentation and secure overlay networks
• Separate encryption keys per tenant
• Resource quotas and fair scheduling
• Tenant-specific monitoring and alerting
• Data residency controls for compliance

9. Observability and Incident Response

Comprehensive monitoring is essential for security operations:

Key Metrics:

• Authentication failures and anomalous access patterns
• Tool execution frequency and parameter analysis
• Resource consumption per tenant/user
• Error rates and latency distributions
• Cost attribution for LLM token usage

Security Event Correlation:

• SIEM integration for centralized analysis
• Machine learning for anomaly detection
• Automated response to common attack patterns
• Forensic data retention for investigations

Potential Implementation Recommendations to Consider

1. Security Architecture Principles

Apply zero-trust principles to all MCP interactions:

• Authenticate every request
• Authorize based on least privilege
• Encrypt all communications
• Log all activities
• Monitor continuously

2. Integration with MCP Gateway and Registry

The MCP Gateway and Registry project already includes an authentication server in its architecture. A natural extension would be to add a dedicated security server that implements many of the controls discussed in this document:

┌─────────────┐     ┌─────────────────────────────────┐     ┌─────────────┐
│ MCP Client  │────▶│         MCP Gateway             │────▶│ MCP Server  │
└─────────────┘     │                                 │     └─────────────┘
                    │  ┌──────────────┐              │
                    │  │ Auth Server  │              │
                    │  ├──────────────┤              │
                    │  │• OAuth 2.0   │              │
                    │  │• Token Mgmt  │              │
                    │  │• Access Ctrl │              │
                    │  └──────────────┘              │
                    │                                 │
                    │  ┌──────────────┐              │
                    │  │Security Server│              │
                    │  ├──────────────┤              │
                    │  │• Input Valid │              │
                    │  │• Rate Limits │              │
                    │  │• Tool Verify │              │
                    │  │• Audit Logs  │              │
                    │  └──────────────┘              │
                    └─────────────────────────────────┘

This security server could provide:

• Real-time payload inspection and validation
• Tool signature verification
• Rate limiting and quota enforcement
• Anomaly detection for prompt injection
• Comprehensive audit logging
• Integration with vulnerability scanning pipelines

3. Security Governance

Establish clear processes for:

• Security review of new MCP servers before registry inclusion
• Automated vulnerability scanning in CI/CD pipelines
• Security incident response procedures
• Regular security assessments of registered servers
• Compliance audit trails

Next Steps

This purpose of this discussion is to outline the numerous security considerations for MCP deployments at enterprise scale. Here's what comes next:

1. Prioritize Implementation: Identify critical controls like input validation, rate limiting, and basic vulnerability scanning and then iteratively improve from there.

2. Reference Implementation: Based on community feedback, selected security features from this analysis will be considered for inclusion in the MCP Gateway and Registry project to provide a reference implementation that others can build upon.

3. Feedback Loop: As organizations implement these recommendations, sharing lessons learned will help refine and improve security practices for the entire ecosystem.

By applying established security practices from API gateways, microservices, and container orchestration to MCP's specific challenges, we can build a secure foundation for enterprise MCP deployments.

Reference Materials

Resource	Description
Red Hat: Understanding MCP Security Risks	Comprehensive analysis of MCP security risks and controls
MCP Server Security Nightmare	Real-world security concerns and attack scenarios
Facebook Pysa Security Tool	Static analysis tool for Python security vulnerabilities
MCP Security Best Practices	Official MCP specification security guidelines
AWS MCP Security Documentation	AWS-specific MCP security considerations
Reddit: MCP Security Discussion	Community discussion on MCP security challenges
Stacklok Toolhive	Tool security and verification platform
Auth0: Secure MCP Server Deployment	Best practices for securing remote MCP servers
Awesome MCP Security	Curated list of MCP security resources
Tencent AI-Infra-Guard	AI infrastructure security framework
AI-Infra-Guard MCP Risks	Specific MCP security risks coverage

[aarora79]

Cc: @asamba-cisco

[westonbrown]

@aarora79 awesome outline! Wanted to just add the following points...

MCP Tool Scanning Requirements

With the use of open source and developer built mcp servers security groups require a scanning solution to ensure no additional risk is being exposed. Current open source solution like MCP-scan from Invariant Labs provides both static and dynamic scanning capabilities, but it relies on external API calls for analysis raises privacy concerns for enterprise deployments. Enterprise environments need:

• Fully offline scanning capabilities with comparable accuracy to cloud-based solutions
• Integration with existing SAST/DAST pipelines rather than standalone tools
• Tool behavior fingerprinting that can detect anomalies without phoning home via a SaaS 3rd party provider
• Version-controlled tool manifests with cryptographic signatures for change detection

Static scanning alone is insufficient. We ideally need:

• Behavioral sandboxing during tool registration to verify declared vs actual functionality
• Runtime policy enforcement that can adapt based on observed agent behavior patterns
• Context-aware rate limiting that considers the full delegation chain, not just the immediate caller

These controls should be implemented at the gateway level to provide consistent enforcement without requiring changes to individual MCP servers.

Continuous Validation

We should have continuous reassessment throughout agent interactions. Per-Request Authorization: Re-validate authorization for every MCP request, not just at the beginning of a session.

Key gaps:

• Tool behavior can evolve post-registration through updates or configuration changes
• Context accumulation across long-running sessions can alter risk profiles
• Multi-hop scenarios require trust reassessment at each delegation boundary

Ideally need guidance for:

• Behavioral drift detection comparing current tool execution against historical baselines
• Risk-based step-up authentication when sensitive thresholds are crossed mid-session
• Session risk scoring that adapts based on accumulated context and actions

Tool Behavior Mutation and Rug Pulls

Tools that change after you've approved them from a security perspective can be pretty scary. While some clients require users to explicitly approve tool integration on installation, the package or server-based architecture of MCP allows for rug pulls - where a malicious server can change the tool code description after the client has already approved it. For example, in strands-agents think about meta tooling when using the editor and loader tool that can dynamically generate tools at execution.

This creates:

• Trust decay where initial security reviews become meaningless over time
• Behavioral drift that's invisible to users but exploitable by attackers
• Supply chain time bombs waiting to activate after gaining widespread adoption if the custom tools persist

Mitigation needs continuous verification, not just point-in-time approval.

[maitreya1975]

I think this document should focus on the security issues and concerns that are specific to MCP Gateways and MCP Registries, and the controls that can be implemented in these two systems to mitigate these concerns.

As an example of a concern that I think is out of scope is "1. Supply Chain Security" for reasons such as:

• This is a more general concern for software procurement and development is not unique to MCP servers.
• There are many ways to scan software at multiple levels, and I think if the Gateway / Registry requires certain scan artifacts to onboard servers that can limit the flexibility for Enterprises that use a variety of tools and processes.

Ultimately, it comes down to a matter of trust: do we trust the Gateway Administrator to onboard only trusted 'servers'?

Making an analogy with API Gateways: the API Gateways place the responsibility on the Gateway Administrator to trust the back-end systems that they onboard. How the Administrator trusts the systems is out of scope of the API Gateway: it could be through software scans, enterprise agreements, whatever.

A similar security model can carry over to the MCP Gateway.