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Best Practices to Secure Model Content Protocol (MCP) Systems

Explore the best practices for MCP security in 2025. Learn how to secure AI agents, control API execution, protect memory, and improve visibility in autonomous workflows.

Bhagyashree

Bhagyashree

Jul 22, 2025

MCP Security Best Practices
MCP Security Best Practices

Anthropic's release of the Model Context Protocol has resulted in rapid adoption, with many companies introducing their own MCP servers to enable AI access to their data. While this expands AI capabilities, it also creates significant security risks. MCP servers can accidentally expose sensitive data from storage tools, CRM, and emails. Even with high-end security, cyber attackers can exploit it by conducting sophisticated attacks, such as prompt injection, to steal credentials. To prevent such vulnerabilities, security teams should establish best practices and reevaluate their current security strategies to mitigate risks.

This blog outlines MCP Security best practices for effectively addressing MCP risks.

What is Model Context Protocol (MCP) in Cybersecurity?

Model Context Protocol is an innovation for AI-driven cybersecurity operations, enabling the smooth integration between AI models and security tools. Traditional API integrations depend on custom code and manual workflows, which restrict scalability. MCP can tackle this with a standardized, self-describing framework. It lets AI to discover and utilize security resources without complex configurations.

MCP Compliance and Regulatory Risks Explained

While Model Context Protocol improves AI responsiveness and capability, it also raises regulatory concerns for security teams and developers. Here's a breakdown of a few of the important regulatory considerations to look for:

Data Privacy Considerations

MCP servers provide AI systems to handle large amounts of sensitive data, including customer information and proprietary business knowledge. This approach raises concerns about data privacy laws, such as the CCPA and GDPR. Organizations must make sure there is transparent data handling by obtaining explicit user consent before processing or accessing any data.

Strong security measures are important to prevent breaches or unauthorized access, as AI decisions based on sensitive data can expose businesses to liabilities. Regular legal reviews are very crucial to ensure that MCP implementations comply with international privacy regulations.

Intellectual Property Rights

MCP enables broad access to data and tools, and intellectual property (IP) issues can arise as a result. Companies must verify that any third-party software that has gained access through MCP is in compliance with licensing agreements in place to prevent copyright violations. Data ownership should also be clarified, especially when multiple stakeholders contribute to AI development, by defining who holds the rights to the models and their outputs.

Besides this, businesses must ensure proper attribution when combining functionality or data from different platforms. If they miss, it could result in legal penalties.

Liability Issues

The integration of MCP servers raises complex questions about accountability when AI systems act independently. If an AI makes a decision that causes loss or breaches data security, determining who is responsible for it, the developer, end-user, or deploying organization, can be challenging. Negligence claims may arise from poor design, implementation drawbacks, or inadequate data management practices, which can lead to significant issues.

To mitigate these risks, businesses should establish explicit and transparent provisions in contracts and maintain rigorous documentation and regular audits of their MCP systems. This approach helps to maintain accountability and safeguards against probable challenges.

Regulatory Guidelines

As governments create regulations for AI and data use, MCP implementations should mandatorily align with evolving compliance standards. Organizations need to monitor evolving frameworks, such as the EU's AI Act, which establishes guidelines for ethical AI operations. Cross-border data transfers also add difficulties as different regions impose varying legal requirements on data transfers.

To ensure compliance, businesses must implement regular auditing and reporting mechanisms that facilitate the tracking of MCP server activities and adherence to relevant laws.

Top 10 MCP Security Best Practices

It is essential to implement best practices that are crucial for the security and protection of MCP systems. Below are the key MCP security best practices explained.

Top 10 API Security Best Practices
  1. Network Segmentation and Micro Segmentation

Segregate MCP servers by VPC subnets or VLANs with rigorous filtering. Deploy service meshes for controlling identity-related traffic. Implement mTLS encryption and apply WAFs and API gateways for deep inspection (DPI) to limit suspicious activities and risky payloads.

  1. Continuous Monitoring and Validation

Reverify each and every MCP request with per-request authorization. Apply user and entity behavior analytics (UEBA) for threat detection, and upgrade authentication for high-risk actions. Continuously monitor all sessions and adapt security measures to address emerging behaviors and threats.

  1. Enable OAuth 2.0+ Implementation.

Utilize strong client authentication like mutual authentication (mTLS), JWT, and implement multi-factor authentication for users. Issue temporary scoped tokens and rotate keys at regular intervals. Prevent token theft through DPoP or mTLS binding and apply audience limits for resource-specific access.

  1. Application Gateway Security Controls

Use stringent protocol validation for MCP traffic. Detect significant security risks, such as prompt injection and tool poisoning. Implement rate limiting, bot detection, and tracing to prevent DoS attacks and conduct an audit for all responses and requests.

  1. Integration of Threat Intelligence

Subscribe to AI-specific threat feeds and share indicators with security communities. Adopt threat intelligence to identify high-risk threats and inform red team exercises, analyzing MCP defenses against emerging attacker methods.

  1. Automate SecOps

Automate important security tasks, such as security patching, configuration drift detection, and access reviews. Utilize security orchestration, automation, and response (SOAR) tools to trigger automatic containment actions, such as tool isolation or firewall updates, which reduce response times and ensure the consistent application of security policies.

  1. Host Based Security Monitoring

Implement EDR and HIDS on the MCP host machines. Monitor the process, memory, and file changes for suspicious activities or in-memory attacks. Employ file integrity monitoring (FIM) and behavior-based detection rules designed for the MCP environment to detect unique threats.

  1. Zero Trust Security Model

Apply no trust and verify principles. Continuously authenticate and authorize every interaction, regardless of location. Assume no implicit trust even within internal networks due to MCP's dynamic tool interactions and ever-changing environments.

  1. Input and Output Validation

Enforce strict schema validation for MCP messages, reject unknown fields and malformed requests. Implement context-based sanitization, normalize inputs, and use semantic validation to restrict injection, parameter smuggling, and threat mitigation methods effectively and adequately.

  1. . Operational Security for MCP

Ensure that you log all MCP events centrally in a SIEM by adding correlation and alerts for malicious activities. Maintain audits and develop essential incident response playbooks for incidents such as data exfiltration, tool poisoning and unauthorized access.

Final Thoughts

Lastly, security teams and organizations must ensure that MCP systems remain secure and protected from emerging attack vectors. Akto.io has got you covered in tackling this new wave of MCP security risks by introducing the industry's first MCP Security Platform for modern AppSec teams. It is designed to protect Model Context Protocol servers with capabilities such as MCP server discovery, full endpoint visibility, live threat detection, real-time monitoring, deep vulnerability testing, and more. Akto's MCP security solution is designed for modern AI stacks, which enables you to detect shadow MCPs, audit AI agent activity, and assist security teams in mitigating threats at the earliest opportunity.

Want to be an early adopter for Akto MCP security? Connect with our security experts today or book a MCP security demo today.

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