MCP Server Security: Choosing the Right Authentication for Your Threat Model

As MCP servers emerge as the standard interface between AI models and external systems, authentication becomes critical—not an afterthought. The threat model differs fundamentally from traditional APIs: compromised AI agents can execute destructive operations with elevated permissions, demanding stronger token scoping and audit capabilities. This guide breaks down three dominant authentication patterns—API keys, OAuth 2.0, and Mutual TLS—with implementation details and security analysis to help you select the right approach for your specific threat model.