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MCP Security Blind Spots: The API Risk

Originally published on: December 2, 2025
▼ Summary

MCP is fundamentally different from a standard API, as it can cause arbitrary, untrusted code to run in sensitive environments, requiring a completely different security model.
– A key misunderstanding is assuming vendor reputation ensures security, but even reputable companies’ MCP servers have had vulnerabilities, like prompt injection issues found with GitHub and Atlassian.
– Organizations often lack centralized governance, leading to risks like shadow MCP deployments and server sprawl, which expand the attack surface without security team oversight.
– Implementing strong identity management and access controls for MCP is a major operational challenge that teams underestimate, as the protocol lacks built-in solutions for authentication and enterprise operations.
– Using an MCP gateway is presented as an essential governance solution to create internal registries, standardize authentication, manage tokens, and prevent risks like tool impersonation attacks.

A critical security challenge emerges as organizations integrate the Model Context Protocol (MCP) into their AI workflows. The fundamental risk stems from treating MCP like a standard API, which creates dangerous blind spots. Unlike traditional APIs, MCP servers inject executable text directly into large language models, influencing their behavior in ways that are difficult to inspect or control. This unique dynamic demands a specialized security approach, as conventional API security frameworks are ill-equipped to handle the specific threats posed by this protocol.

One of the most common and hazardous misunderstandings is equating MCP communication with standard API transactions. This assumption is flawed because MCP can cause arbitrary, untrusted code to execute within sensitive environments. LLMs interpret text as instructions, and the context provided by an MCP server directly shapes those instructions. A critical distinction is the inability to pin or review trusted versions. Each connection fetches the latest metadata from the server, meaning you are accepting runtime-provided text without prior inspection. A server that appears benign today could, in a future connection, inject malicious context, a scenario akin to a “rug pull.” These inherent risks are unique to the protocol.

Another area of confusion involves client trust. Security teams might incorrectly assume they can trust all clients registering with their MCP servers, which is why the specification is evolving to require more robust client identification. Dynamic client registration and OAuth alone are insufficient for establishing strong identity assurance. Furthermore, there’s a tendency to conflate vendor reputation with architectural security. Just because a server comes from a reputable SaaS provider does not guarantee its safety. Researchers have already identified prompt injection vulnerabilities in MCP servers from major technology companies, proving that no source is inherently immune.

It is vital to remember that MCP is a protocol, not a product, and it offers no built-in trust guarantees. The protocol defines a communication language but does not solve for authentication, identity management, enterprise operations like audit trails, or infrastructure concerns such as hosting and rate limiting. These critical components must be implemented separately by the adopting organization.

As MCP deployment scales within companies, significant governance blind spots appear. A common issue is the lack of centralized observability and controls. Without an internal MCP registry and formal approval processes, organizations invite two major problems: shadow MCP and server sprawl. Shadow MCP occurs when employees introduce unauthorized servers unknown to IT and security teams. Server sprawl results from the accumulation of duplicate, unnecessary, or unused servers, each expanding the attack surface. Local MCP deployments are particularly risky, as they may have access to sensitive on-device credentials, API tokens stored in plain text, and critical files, creating a lucrative target for exploitation.

To verify the authenticity of both MCP servers and invoking models, organizations must establish rigorous review and approval processes for all clients and servers. Security-conscious teams should mandate OAuth 2.1 with PKCE, ensuring the use of regularly rotated, finely-scoped, and securely stored tokens. Using simple bearer tokens is risky, as they are often stored in plain text. Another subtle threat is tool impersonation, where malicious actors create tools with names similar to legitimate ones, tricking the AI model into selecting the wrong tool and potentially leading to data exfiltration or corruption.

Implementing an MCP gateway is a foundational step for mitigating these risks. A gateway enables the creation of an internal registry, standardizes authentication flows, ensures proper token rotation, and allows for allowlists and blocklists. It can also add namespaces to tools, helping AI models distinguish between them correctly.

Practitioners frequently underestimate the operational effort required for secure MCP deployment, particularly around identity and access management. The complexity of integrating MCP with existing enterprise identity infrastructure is a heavy lift. While flashy attack vectors get attention, the ongoing, intricate work of managing identities for both human users and AI agents is often overlooked. A proper MCP gateway should require individual user credentials for accessing servers, preventing the overuse of shared service accounts that lack auditability.

Looking ahead, regulatory compliance will become the most significant governance challenge as MCP use expands across regulated industries. Organizations will face internal and external pressure to implement strict, granular controls to protect sensitive data like personal information, financial records, and health data. This will necessitate safeguards and auditable logs of AI access and actions. An MCP governance platform is becoming a non-negotiable tool, much like sophisticated email security is today. Emerging best practices will include the early adoption of policy-based access controls for scalable and granular permission management, and a shift toward managed, cloud-hosted MCP deployments within enterprises, reducing reliance on purely local implementations.

(Source: HelpNet Security)

Topics

mcp trust model 95% protocol governance 92% mcp vs apis 90% mcp gateways 89% runtime security 88% identity management 87% Regulatory Compliance 85% oauth implementation 83% shadow mcp 82% prompt injection 81%