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An MCP server’s tool list defines what a host can ask it to do; the server process’s permissions define what it can actually do. Keep both narrow: expose only intended operations, validate each tool’s arguments, and reserve stdout for the stdio protocol. Schemas and annotations clarify intent, but they do not sandbox a handler or guarantee safe effects.
Start with the server’s real authority
Before registering tools, identify what the server process can reach: files, APIs, shell commands, databases, and network destinations. A tool such as read_project_file may look narrow in its name, but if the process can read the entire machine, its actual authority is broader than that name suggests.
Hosts can discover and call the tools a server registers, including their names, descriptions, and input schemas. Treat that list as a capability surface: define only operations the server is meant to expose, and limit the process itself to the resources those operations require. The MCP TypeScript SDK v2 overview describes tool registration and the current v2 line, which implements the 2026-07-28 specification.
Make each exposed operation specific
- Use names and descriptions that say what an operation does, rather than offering broad tools such as “run command” or “access files.”
- Keep each tool’s arguments limited to what that operation needs.
- Restrict paths, identifiers, and destinations in application logic to the intended scope.
- Make destructive operations explicit in their names and interaction design; add human approval where the application requires it.
Use schemas to define and check inputs
A tool schema tells the host what arguments are expected and gives the server a basis for rejecting malformed calls. In the TypeScript SDK v2, the supplied input schema is used to derive JSON Schema, and invalid arguments are rejected before the handler runs. The TypeScript SDK overview and first-server guide document that pattern. The Java SDK server documentation also describes default input validation, with configurable JSON Schema validation and schema meta-validation.
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These examples are SDK- and version-specific, not a guarantee of identical behavior in every MCP implementation. Check the documentation for the SDK and version you deploy. A useful schema should make required values, types, and allowed ranges explicit; application logic should also reject values that exceed the intended resource scope.
Validation is not authorization
A structurally valid argument can still cause an unsafe effect. A valid path may point outside an allowed directory unless the handler checks it; a valid operation may still affect a resource the caller should not control. The SDK’s pre-handler validation checks input shape, not every downstream permission or effect. Enforce authorization and resource checks at the sensitive operation as well.
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Keep stdio dedicated to the protocol
With stdio transport, the host launches and owns the local server process, sends JSON-RPC requests on stdin, and reads responses on stdout. That makes stdout a protocol channel, not a place for ordinary logs. Send diagnostics, startup messages, and debug output to stderr; a stray line on stdout can make the host unable to parse the exchange. The MCP TypeScript SDK v2 guide to serving over stdio states that “stdout is the JSON-RPC channel” and illustrates how a debug line before a response breaks the stream.
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Choose transport for the deployment boundary
For a server running as a local child process, stdio is the documented transport: the host launches the process and communicates through its standard input and output. For a shared network service, the TypeScript SDK documentation points to HTTP serving instead. Neither choice is a safety control by itself. Decide based on who should connect, where the process runs, what permissions it receives, and what network authorization and host controls are required. See the SDK overview and stdio guide for the transport descriptions.
Treat annotations as descriptive hints
Tool annotations can communicate properties such as a read-only intent, but they do not enforce those properties. MCP project guidance says clients should treat annotations as untrusted unless the server is trusted. A handler marked with a read-only hint can still modify a file if its implementation does so.
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The MCP project’s 2026-03-16 discussion of tool annotations frames them as risk vocabulary, not controls. Use actual permission checks, process isolation, or an approval step for effects that need enforcement; do not rely on annotation metadata to stop a mistaken or malicious handler.
Inspect the server during development
The official first-server guide describes using MCP Inspector to launch a supplied command, connect over stdio, inspect registered tools, and call them. This is useful for checking what the server exposes and whether calls behave as expected during development; using Inspector is not, by itself, a security audit. Consult the MCP TypeScript SDK first-server guide for its local workflow.
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Keep protocol updates separate from local isolation
The MCP project’s 2026-07-28 specification announcement discusses authorization hardening, including issuer validation. Protocol authorization changes do not isolate a local process or constrain a handler’s access to files, commands, or networks; those remain implementation and operating-system concerns.
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