Zotero MCP: Your Citation Library as an Agent Tool

A reference manager becomes much more useful when the agent can ask it directly.

Zotero MCP connects your Zotero library to AI assistants through the Model Context Protocol. The agent can search the library, retrieve metadata and full text, inspect annotations, and export BibTeX. When you configure write access, it can also add or update items.

Package: zotero-mcp-server

Why it matters

A Zotero library is accumulated judgment: years of deciding what was worth keeping, which collection it belonged in, which passages deserved a highlight. Without a connection, an agent writes around that record, drawing on its training-data impression of the field instead - the path by which plausible but unverifiable citations enter drafts.

Connecting the library changes what can be checked. Citation keys come from your bibliography rather than pattern-matching; a claim can be tested against the paper you actually read; the annotations you made at reading time resurface at writing time. The library remains the source of record, and the agent finally treats it as one.

Tools

Host support

Zotero MCP is a standard MCP server. It works anywhere a host can launch Python tools over stdio.

The server supports local, web, and hybrid modes. Local mode is best when Zotero is installed on the same machine and you want offline reads. Web or hybrid modes make sense when writes or cloud-library access matter.

Install

Two practical routes:

• Via Carrel — run /carrel-setup and say yes when the interview asks about Zotero or citation-library integration. Carrel adds the MCP at project level and prompts for the relevant setup.
• Manually — install the server and register it with your MCP host.

You need Python 3.10 or newer, and Zotero 7 or newer if you want local full-text access.

Default install:

uv tool install zotero-mcp-server
zotero-mcp setup

zotero-mcp setup writes the host configuration for you. pip and pipx install the same package.

With heavier extras:

uv tool install "zotero-mcp-server[semantic]"   # embeddings + vector index
uv tool install "zotero-mcp-server[pdf]"        # PDF outlines, EPUB annotations
uv tool install "zotero-mcp-server[scite]"      # citation tallies, retraction alerts
uv tool install "zotero-mcp-server[all]"        # all of the above

The base install is the right default for most researchers. Add extras only when you need semantic search, PDF outline extraction, EPUB annotation support, or citation-intelligence features.

Let Zotero answer

Nothing works until Zotero is willing to be asked. In Zotero's settings, under Advanced, turn on Allow other applications on this computer to communicate with Zotero, and leave Zotero running while you work.

Register it with the host

For Claude Desktop, zotero-mcp setup does this for you. For Claude Code, the server goes in ~/.claude.json:

{
  "mcpServers": {
    "zotero": {
      "command": "zotero-mcp",
      "env": {
        "ZOTERO_LOCAL": "true"
      }
    }
  }
}

ZOTERO_LOCAL: "true" on its own is enough for reading, and reading is most of the work. The local API cannot write, so writes travel over Zotero's web API instead: add ZOTERO_API_KEY and ZOTERO_LIBRARY_ID (your numeric user ID, printed on the same Zotero security settings page that issues the key) and the server runs hybrid, reading locally and writing over the web.

Two traps are worth naming. Environment variables set in the shell you launch the host from will override whatever the config file says. And GUI applications do not reliably inherit your shell PATH, so if a host reports that it cannot find zotero-mcp, give it the absolute path that zotero-mcp setup-info prints.

The CLI, for agents with a shell

The same package installs zotero-cli, a standalone terminal interface to the library that needs no AI assistant at all. This matters more than it first sounds. An agent that already has a shell, such as Claude Code or Codex, can call the CLI directly, and a shell command costs far fewer tokens than the equivalent MCP tool schemas, which occupy context whether or not the agent ends up using them.

zotero-cli search "attention mechanisms" --mode semantic
zotero-cli get metadata ABC123 --format bibtex
zotero-cli add doi 10.1038/s41586-021-03819-2 --collections "Reading List"
zotero-cli ann search "boundary condition"

Adds are idempotent by default: run the same add twice and the second run files the existing item into any collections it was missing rather than creating a duplicate. Both surfaces read the configuration that zotero-mcp setup already wrote, so there is nothing further to arrange.

Full documentation, including the ChatGPT setup path, lives at the Zotero MCP docs.

Part of Research Memex

Zotero MCP is the citation-library counterpart to the document and memory tools:

• Carrel sets it up when the interview surfaces Zotero.
• MinerU turns difficult PDFs into AI-ready text; Zotero MCP keeps the reference graph and annotations reachable.
• Memex Plugin remembers why papers mattered in a session; Zotero remains the bibliographic source of record.
• Research Scanner can feed new candidates into Zotero for durable tracking.

Use Zotero MCP when the answer depends on what is actually in your library. You can check citation coverage, what you already read, which annotations support a claim, or whether a draft cites the right sources.