What’s the Difference Between MCP and an API?

TL;DR:

MCP isn’t an alternative to APIs — it’s a new layer that governs how autonomous agents access existing APIs securely, with identity, delegation, and audit built in. APIs expose functionality. MCP governs who can use it, how, and under what conditions — especially in agent-based, multi-tenant environments.

Introduction

As autonomous agents (like GPT-based copilots, scripts, or SaaS-integrated LLMs) become more common, the question arises:

Do we need a new protocol to govern how they access our systems?

Enter MCP: the Machine Client Protocol.

But wait — isn’t that what an API already does?

Let’s unpack the difference.

🔧 What Is an API?

An API (Application Programming Interface) is a set of defined endpoints and rules that let one software system interact with another. APIs expose functionality, data, and services. They define:

• What data can be sent or retrieved

• Which operations are available (CRUD, etc.)

• Expected formats and responses

But APIs don’t define:

• Who the requester really is (agent identity)

• What level of access they should have (delegation, scope)

• How their access is governed, monitored, or revoked (audit/logging)

• Multi-tenant controls for agents acting on behalf of users

🤖 What Is MCP?

Machine Client Protocol (MCP) is an emerging standard designed for agent-based access. It wraps around APIs and provides the missing infrastructure for agent identity, access control, and audit.

MCP is not about creating new endpoints. It’s about:

• Giving agents (not just apps or humans) verifiable identities

• Enabling delegated authority (i.e. an end-user authorizes an agent to act on their behalf)

• Issuing tokens with limited scope and expiry

• Ensuring auditable, revocable, and granular access

🆚 MCP vs. API: The Key Differences

🧠 Why This Matters Now

Modern apps are increasingly being accessed not just by users, but by autonomous agents: GPT plugins, automation bots, AI copilots, etc.

Traditional API models weren’t designed for this — leading to:

• Over-permissioned service accounts

• Hardcoded keys that can’t be traced

• No way to see which agent did what, or why

MCP solves that by defining identity, delegation, and access for this new class of actor.

🚀 Real-World Analogy

Think of your API like the door to your office.
Right now, most people (or bots) just have a generic key.

MCP is like issuing named, digital ID badges with:

• Custom permissions

• Automatic expiry

• Access logs

• Delegation: “Matt’s assistant can enter the meeting room, but not the finance department”

🔒 Prefactor & MCP

At Prefactor, we’re building the first authentication layer built specifically for MCP:
✅ Agent identity
✅ Scoped access
✅ Revocable tokens
✅ Full audit trail

If your customers — or their agents — need secure access to your platform, you need more than just an API.

You need control.

✅ Key Takeaways

• MCP is not an API replacement — it’s an access layer for agents.

• It defines identity, delegation, scope, and audit — everything APIs alone don’t.

• As AI agents proliferate, MCP will become the new standard for secure, multi-tenant machine access.

Sign up for an MCP consultation or a Prefactor Demo today.