Best practices for securing and governing tool access in an MCP hub

MCP tools are active endpoints that can read, write, or trigger actions across multiple systems. When these tools are orchestrated across different MCP servers, the hub becomes the central point of decision-making for what’s accessible, by whom, and under what conditions.

Without clear governance, this openness can quickly become a liability. A single misconfigured permission or an unmonitored tool call could expose sensitive data, break compliance rules, or trigger unintended actions. The risk multiplies when multiple agents, teams, and environments are connected to the same hub.

Understanding the governance challenge in MCP hubs

An MCP hub acts as the coordination layer for multiple MCP servers, each potentially exposing dozens of tools. These tools can range from internal APIs and databases to third-party services and public endpoints. The more powerful the tools, the greater the need to control how and when they’re used.

The governance challenge comes from the diversity of participants in the hub:

• Multiple agents may be running different workflows simultaneously
• Multiple teams may share the same underlying tool infrastructure.
• Multiple trust levels exist across tools, some are fully internal, others come from unverified or external sources.

In this environment, risk doesn’t only come from malicious actors. A well-intentioned agent could call the wrong tool with the wrong parameters, or a developer could unknowingly give a model access to a tool it shouldn’t use. Without central governance, issues like these can cascade across the system.

An effective MCP hub must account for these realities, putting in place the right structures to keep access aligned with organizational policy while still enabling flexibility for builders.

Best practices for securing and governing tool access

Governance in an MCP hub is a combination of policy, infrastructure, and ongoing monitoring. Below are the key practices that help keep tool access secure while ensuring teams can still move quickly.

Enforce the principle of least privilege

Only give each role, workspace, or team access to the tools they genuinely need. Avoid exposing an entire tool registry to everyone, limit visibility so unneeded tools are invisible by default. This reduces the risk of accidental misuse and narrows the blast radius if a credential is compromised.

Centralize authentication and authorization

Unify how tool credentials are issued, stored, and validated. Use OAuth or a centralized API key manager at the hub level rather than scattering credentials across individual MCP servers, making it easier to rotate keys, revoke access, and enforce consistent security standards.

Monitor and audit tool usage

Log every tool invocation with detailed context:

• Which agent or user triggered it
• Which MCP server and tool was accessed
• What parameters were passed
• The resulting output or action

Review logs regularly to detect anomalies, identify patterns of risky usage, and feed insights back into access policies.

Apply guardrails

Intercept and inspect requests before they reach sensitive tools. Use input filtering, output sanitization, and policy checks to block malicious or non-compliant requests. Centralized guardrails ensure enforcement is consistent across all MCP servers and tools.

Implement regional and compliance controls

If tools handle regulated data, enforce geographic restrictions and compliance-based routing. For example, GDPR-bound tools should only run on EU-hosted infrastructure and avoid cross-region data transfer. Always align tool endpoints with your organization’s compliance requirements.

Building governance into your MCP hub from day one

The easiest way to secure and govern tool access is to design for it before the first MCP server connects to your hub. Retrofitting governance later often means rewriting policies, migrating credentials, and reworking workflows, changes that are harder and riskier to make once the hub is already in production.

A governance-first approach starts with:

Clear access models – Define how tools will be grouped, who can request access, and how approvals are handled.

Integrated security controls – Bake in authentication, authorization, and guardrails at the hub layer rather than leaving them to individual servers.

Trust boundaries – Separate environments for development, testing, and production to prevent accidental cross-environment access.

Compliance awareness – Map tools and their data flows to regulatory requirements before they go live.

This upfront investment ensures that as your MCP hub scales, whether it’s connecting a few servers or dozens and security & governance remain consistent. It also sets the stage for automation, making it easier to apply policies and access controls programmatically.

The role of observability in secure tool access

Governance policies only work if you can see whether they’re being followed. In an MCP hub, observability is the layer that turns access controls into enforceable, measurable reality.

A strong MCP observability setup should:

Track every request – Capture who triggered the tool, from which MCP server, and with what parameters.

Provide historical context – Allow teams to review past activity during audits, security reviews, or incident investigations.

Connect with enforcement – Link monitoring alerts to automated responses, such as throttling a misbehaving workflow or suspending a compromised credential.

By making tool usage transparent, observability not only helps detect threats early but also strengthens trust between teams sharing the same MCP hub. It turns governance from static rules into an active feedback loop to adapt to new risks as the hub evolves.

Build with these best practices

The teams successfully building agents will be the ones that treat governance as part of their hub’s architecture from day one. Done right, it empowers innovation instead of slowing it down.

And with solutions like Portkey’s MCP hub, those governance principles can be built into the infrastructure itself, so every tool call is as safe as it is powerful.

If you'd like to see what we're building, book a demo with us.