MCP Server Architecture and Design

Model Context Protocol security AI infrastructure protection
Brandon Woo
Brandon Woo

System Architect

 
November 28, 2025 7 min read

TL;DR

This article dives deep into the architecture and design of Model Context Protocol (MCP) servers, a vital component for secure ai infrastructure. We'll explore the core components, design principles, and security considerations involved in building robust and quantum-resistant mcp servers. Also, we'll highlight best practices for safeguarding your ai deployments against emerging threats like tool poisoning and prompt injection.

Understanding the Core Components of an MCP Server

Alright, let's dive into the guts of an MCP server. Ever wonder how these ai things actually do stuff? It all starts with understanding its core components, kinda like knowing the engine in your car before you try to win a race, ya know?

First up, we got the host. Think of it as the ai application itself – like claude, for instance. The Model Context Protocol notes that the host is responsible for a lot. It's creating and managing those client instances. Plus, it's calling the shots on permissions, security policies, and making sure users are actually authorized. It's also where the ai/llm integration magic happens. (There's Only One AI, Let's Clear Up the Confusion Around ...) And you know, making sure everything plays nicely with context aggregation. Context aggregation is basically how the MCP server collects and synthesizes information from various sources – like user inputs, previous conversation turns, and even external data – to build a comprehensive understanding of the current situation. This unified context is then used to inform the ai's responses and actions.

Then there's the client. Each host spins up clients, and each client has a one-to-one relationship with a server instance. That's key. intuz.com mentioned it's the active component that communicates with the server using JSON-RPC messages. JSON-RPC is a lightweight remote procedure call protocol that uses JSON as its data format. It's used here because it's simple, widely understood, and efficient for sending requests and receiving responses between the client and server. The client is negotiating protocols, exchanging capabilities and routing messages back and forth. It keeps the conversations with each server separate, which is pretty important for security, if you ask me.

And lastly you have the servers. These are the guys exposing resources, tools, and prompts. The actual doers, really. Model Context Protocol tells us that servers operate independently and have focused responsibilities. They're like microservices, each doing its own thing. They gotta respect security constraints, though, and they can be local processes or even remote services.

Diagram 1
The above diagram shows how a single MCP Host can have multiple MCP clients, with each client instance paired with a single MCP Server instance. A host can manage multiple such pairings.

MCP is built on the principles of servers being easy to build, highly composable, and unable to snoop on other servers. Oh, and features can be added progressively without breaking everything. Not bad, right?

Understanding these core components is vital, but it's just the tip of the iceberg.

Key Design Principles Shaping MCP Server Architecture

Okay, so you're thinking about diving into MCP server design? Cool. It's not just about slapping some code together; it's about setting up a solid foundation. Think of it like building a house – you wouldn't skip the blueprints, right?

One thing they really hammered home in the design is how easy it should be to build these servers. The idea is that the ai host handles the complex orchestration, so your server can focus on doing one thing really well.

  • This means less implementation overhead. You're not wrestling with a ton of boilerplate code.
  • Servers stick to well-defined jobs. Each server should be like a specialized tool in a workshop, not a Swiss Army knife.
  • Clear separation of concerns is key, too. You want code that's easy to read and maintain, not a tangled mess.

For example, imagine a security analyst wants to build a server that scans files for malware. They don't wanna deal with all the ai plumbing, they just want to focus on the scanning part.

Another big deal is composability. The whole point of mcp is that you can mix and match servers to create more complex ai systems. It's like using Lego bricks – each server is a building block.

  • This means the protocol has to be interoperable. Servers need to "speak the same language."
  • A modular design makes it easy to add new stuff without breaking existing integrations.
  • The shared protocol enables interoperability.

Security isolation is also seriously important. Servers shouldn't be able to snoop on each other or access the entire conversation history. It's like giving each server its own private workspace. According to Model Context Protocol, this is achieved by maintaining isolation between server connections and controlling cross-server interactions through the host.

  • The host is responsible for enforcing security boundaries.

Finally, the design allows for progressive feature addition. You don't have to implement every bell and whistle upfront.

  • Start with a minimal core protocol.
  • Negotiate additional capabilities as needed. This means that if a client or server needs a specific function that isn't part of the basic protocol, they can discover and agree to use it. For instance, a server might offer advanced image analysis capabilities, and a client could negotiate to use those capabilities if its task requires it. This negotiation happens through specific protocol messages exchanged during the connection setup or during operation.
  • Servers and clients can evolve independently, which is great for long-term maintainability.

As you can see, these design principles are all about making mcp servers easy to build, secure, and flexible.

Implementing Robust Security Measures in MCP Server Design

Alright, let's talk security – cause ain't nobody got time for their ai servers getting hacked, right? So, how do we keep those pesky bad actors out of our mcp server setups?

First up, capability-based negotiation is key. This is all about setting clear expectations from the get-go. During server initialization, both the client and server need to explicitly state what they can and can't do.

  • The server's gotta say, "Hey, I can do this, that, and maybe that other thing." this includes resources, tools and prompts.
  • The client then needs to respond with its capabilities -- things like sampling support or handling notifications.

Think of it like a handshake – everyone knows what's on the table. And as Model Context Protocol notes, these declared capabilities must be enforced throughout the entire session. It's like, if you say you can't juggle flaming chainsaws, you don't juggle flaming chainsaws.

Listen, you know quantum computers are supposedly gonna break all our encryption, right? That's why post-quantum cryptography is so important. We gotta be future-proof, man! The relevance to MCP servers is that the data exchanged, especially sensitive data like patient records or proprietary business information, needs to remain secure even against future quantum computing threats. Integrating quantum-resistant algorithms into the communication channels ensures the long-term confidentiality and integrity of this data.

  • We need to start implementing quantum-resistant algorithms now in our communication channels.
  • This ensures the long-term confidentiality and integrity of our data.

Next, let's talk access. We need to implement context-aware access management.

  • This means defining restrictions at the parameter level for all mcp operations.
  • It's about enforcing precise permission controls for every action.

Imagine a user wants to query a weather server for a specific city. Instead of just allowing any city, parameter-level restrictions could ensure the user can only query cities within their authorized region. For example, a user might be allowed to query "New York" but not "London" if their access is geographically limited.

And, of course, we need to integrate all this with existing identity and access management (iam) systems.

Imagine a healthcare provider using mcp servers to manage patient data. They need to ensure that only authorized personnel can access sensitive information. By implementing capability-based negotiation and granular policy enforcement, they can restrict access to specific data fields based on user roles. For example, a nurse might have access to basic patient information, while a doctor can access more detailed medical records.

Best Practices for Building and Deploying Secure MCP Servers

Okay, so you've built an mcp server – now what? Well, it's gotta be locked down tight, right?

  • Code reviews are crucial. Have another set of eyes scan the code for vulnerabilities--kinda like a second opinion from a doctor, really.
  • Keep dependencies up-to-date. Outdated libraries? That's an open door for attackers; make sure you're updating regularly!
  • Least privilege is key. Don't give your server more permissions than it absolutely needs.

Think of it like this, if you only give the server the keys to the front door – which might be the ability to read a specific configuration file – the attacker can't get to the safe in the basement – which might be the ability to modify critical system settings. Make sense?

Brandon Woo
Brandon Woo

System Architect

 

10-year experience in enterprise application development. Deep background in cybersecurity. Expert in system design and architecture.

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