When connecting multiple MCP servers, several significant challenges emerge that affect security, performance, and management. These issues are particularly important as the MCP ecosystem continues to evolve and expand.
Tool shadowing represents a critical security risk when connecting multiple MCP servers. A malicious MCP server can override tools from trusted servers, potentially leading to security breaches. This vulnerability is particularly concerning because users may not realize that a malicious server has taken control of a trusted tool's functionality.
Authentication and authorization become more complex in multi-server environments. Without proper security measures:
- A malicious server could shadow or alter commands from trusted servers[2]
- Users might have difficulty distinguishing between legitimate and compromised tool actions
- Stolen authentication tokens could be used to create rogue MCP server instances that appear legitimate[3]
The current MCP ecosystem faces several limitations when connecting multiple servers:
- Port management complexity: In SSE transport mode, each MCP server requires a dedicated port, making it difficult to manage and scale in containerized environments like Kubernetes[1]
- No dynamic extensibility: Most MCP servers require a fixed set of tools defined at startup, with limited support for adding or removing tools at runtime[1]
- Single-tenant design issues: Many MCP servers are designed for single-tenant use with stateful interactions, making them unsuitable for scaling applications or accessing from multiple clients[6]
Implementing proper permission management across multiple connected MCP servers presents significant difficulties:
- There's no straightforward method for defining tool permissions for each agent across multiple servers[4]
- Users need granular control, such as allowing one agent read-only access to certain services while giving write access to others[4]
- The centralization of access to disparate services creates a "keys to the kingdom" scenario where compromising one MCP server could grant attackers broad access to multiple systems[3]
Deploying multiple interconnected MCP servers introduces additional challenges:
- Serverless environment deployment is particularly difficult under the current design[6]
- The most common approach uses long-running containers communicating over SSE, which becomes unwieldy when scaling to a larger number of MCP servers[6]
- Network-level connection problems can arise from firewall restrictions, incorrect routing, SSL/TLS certificate issues, and bandwidth constraints[5]
When multiple tools from different MCP servers are called to perform a single task, new security risks emerge:
- Indirect prompt injection attacks can leverage combinations of tools across servers to perform exploits[7]
- Users may grant permissions to individual tools without understanding the risks when those tools are used in combination[7]
- Authentication data often lacks inline passing support, leading to insecure credential storage on servers[6]
These challenges highlight the need for improved security frameworks, better permission management, and more scalable architectures as the MCP ecosystem continues to mature and expand.
Citations: [1] https://itnext.io/multi-mcp-exposing-multiple-mcp-servers-as-one-5732ebe3ba20 [2] https://www.linkedin.com/pulse/securing-model-context-protocol-mcp-challenges-best-muayad-sayed-ali-sot4e [3] https://www.pillar.security/blog/the-security-risks-of-model-context-protocol-mcp [4] https://www.reddit.com/r/mcp/comments/1jdmsrl/what_are_your_biggest_challenges_when_creating/ [5] https://www.byteplus.com/en/topic/541583 [6] https://www.cortexreply.com/insights/early-challenges-of-utilising-mcp-servers [7] https://hiddenlayer.com/innovation-hub/mcp-model-context-pitfalls-in-an-agentic-world/
Answer from Perplexity: pplx.ai/share