MCP Zotero

MCP Zotero

Note: This is an unofficial community project and is not affiliated with, endorsed by, or supported by the Zotero team or the Corporation for Digital Scholarship. "Zotero" is a registered trademark of the Corporation for Digital Scholarship.

A Model Context Protocol server for Zotero integration. It gives any LLM full access to your Zotero library: search, organize, add papers by DOI, import PDFs, read full-text content, and inject live citations into Word documents.

Originally based on mcp-zotero by Abhishek Kalia. This project has since been extensively rewritten with a new architecture, 15 tools (up from 5), citation injection, PDF management, and Claude skill support.

How it works

The server is designed to be usable by any LLM without external documentation. On connection, it sends workflow instructions via the MCP instructions field, and each tool description includes cross-references and usage guidance. An LLM that has never seen this server before can discover the full workflow — from adding papers to producing a cited Word document — directly from the tool listing.

For advanced use cases (PDF upload policy, citation style guidance, source transparency), a Claude skill is included for Claude.ai Projects. But the skill is optional: the MCP server is fully self-documenting.

Local vs Remote LLMs

LLMs with filesystem access can use all tools directly, including inject_citations which reads and writes .docx files on disk.

LLMs without filesystem access — including Claude Desktop, which connects to MCP but cannot generate files locally — can use the included Claude skill (skills/zotero-skill-mcp-integrations/), which runs citation injection entirely inside a sandbox. MCP tools handle all Zotero API operations; the skill handles document assembly.

Claude Skill Setup (for Claude.ai Projects and Claude Desktop)

1. Download the skill .zip from the latest GitHub Release
2. Extract it and upload the folder to your Claude.ai Project as a skill
3. The skill enables citation injection directly inside the sandbox, without requiring local filesystem access

Setup

Requires Node.js 22 or newer.

The server is listed in the official MCP Registry as io.github.Xevos117/mcp-zotero (starting with the first release after 2.0.2), so registry-aware clients can find and install it from there; the configuration below works with any MCP client.

1. Get your Zotero credentials:

   bash

   # Create an API key at https://www.zotero.org/settings/keys# (enable library read/write + file access)# Then retrieve your user ID:curl -H "Zotero-API-Key: YOUR_API_KEY" https://api.zotero.org/keys/current

2. Set environment variables:

   bash

   export ZOTERO_API_KEY="your-api-key"export ZOTERO_USER_ID="user-id-from-curl"export UNPAYWALL_EMAIL="[email protected]"   # Optional: enables OA PDF lookup via Unpaywallexport UNSAFE_OPERATIONS="none"           # Optional: "none" | "items" | "all" (see below)

Targeting a group library

By default the server targets your personal Zotero library (/users/<ZOTERO_USER_ID>/...). To target a group library instead, set two additional environment variables:

Example for a group library:

ZOTERO_API_KEY=...ZOTERO_USER_ID=12345               # optional for groups: used by get_user_id and per-call library_type="user"ZOTERO_LIBRARY_TYPE=groupZOTERO_LIBRARY_ID=6178978          # the group ID

The API key in ZOTERO_API_KEY must have access to the target group library — generate or scope keys at https://www.zotero.org/settings/keys.

The server refuses to start if ZOTERO_LIBRARY_TYPE=group is set without ZOTERO_LIBRARY_ID, or if a library ID is not numeric.

Per-call library override

Every tool accepts two optional args that override the env defaults for that single call:

• library_type — "user" or "group"
• library_id — numeric library ID

Resolution order: per-call arg > env var > implicit default (user, ZOTERO_USER_ID). library_id must be numeric. Overriding library_type to group on a server configured for a user library requires library_id; overriding to user on a group server without library_id uses ZOTERO_USER_ID.

Note that per-call overrides let the LLM reach any library the API key can access. Scope the key to the libraries you want exposed; deletions remain gated by UNSAFE_OPERATIONS.

This lets a single MCP instance target multiple libraries (e.g., a staging group and a final-output group) without restarting:

// First call targets the staging group{  "tool": "add_items",  "args": {    "items": [...],    "library_type": "group",    "library_id": "5597114"  }}
// Second call targets DART-output (different group){  "tool": "add_items",  "args": {    "items": [...],    "library_type": "group",    "library_id": "6178978"  }}

Environment Variables

Unsafe Operations

By default, the MCP server does not allow any deletion. This is a safety measure to prevent an LLM from accidentally deleting items or collections from your library.

To enable deletion, set the UNSAFE_OPERATIONS environment variable to one of the following values:

Important notes:

• If UNSAFE_OPERATIONS is not set, empty, or set to an unrecognized value, it defaults to none.
• The value is case-insensitive (e.g. ALL, Items, NONE all work).
• delete_items deletes items permanently: the Zotero Web API multi-item DELETE does not move them to the Zotero trash, so they cannot be restored from the desktop client.
• delete_collection removes the collection (folder) only — items inside it are not deleted and remain in your library.
• The all value includes both item and collection deletion because managing collections inherently requires item-level access.

Configuration example:

{  "mcpServers": {    "zotero": {      "command": "npx",      "args": ["-y", "@xevos117/mcp-zotero"],      "env": {        "ZOTERO_API_KEY": "YOUR_API_KEY",        "ZOTERO_USER_ID": "YOUR_USER_ID",        "UNSAFE_OPERATIONS": "items"      }    }  }}

Integration with Claude Desktop

Install as a Claude Desktop extension (one click)

1. Download mcp-zotero.mcpb from the latest release (available from the first release after 2.0.2).
2. Open the file with Claude Desktop (macOS or Windows; e.g. double-click it) and confirm in the installation dialog. The bundle itself is not platform-specific (manifest.json lists macOS, Windows and Linux, and CI runs it on Linux), so other MCPB-compatible clients can install it too.
3. Fill in your Zotero API key and Zotero user ID (see Setup). Optional settings: library type and group ID (for a group library), the email for Unpaywall (open-access PDF lookup) and which deletions are allowed (default: none, see Unsafe Operations).

The extension bundles the server and all its dependencies, so no npm install is needed. It needs Node.js 22 or newer (compatibility.runtimes.node in the manifest): according to the MCPB documentation, Claude Desktop runs Node.js extensions with the runtime that ships with the app. The API key is declared as a sensitive setting (masked input, stored securely by the client). Deletions stay disabled unless you change Deletions allowed in the extension settings.

The extension contains only the MCP server: the Claude skills in skills/ (citation injection inside the sandbox, scientific writing) are installed separately from their .zip files in the same release, as described in Claude Skill Setup.

Manual configuration (any MCP client)

Add to your Claude Desktop configuration (or the equivalent file of another MCP client):

{  "mcpServers": {    "zotero": {      "command": "npx",      "args": ["-y", "@xevos117/mcp-zotero"],      "env": {        "ZOTERO_API_KEY": "YOUR_API_KEY",        "ZOTERO_USER_ID": "YOUR_USER_ID",        "UNPAYWALL_EMAIL": "YOUR_EMAIL"      }    }  }}

Integration with Claude Code

claude mcp add zotero -e ZOTERO_API_KEY=YOUR_API_KEY -e ZOTERO_USER_ID=YOUR_USER_ID -- npx -y @xevos117/mcp-zotero

Add -e UNPAYWALL_EMAIL=... or -e UNSAFE_OPERATIONS=items as needed, and --scope user to make the server available in every project (the default local scope covers only the current project). From a clone of this repository, npx tsx src/server.ts runs the server from source instead (see Development).

Available Tools

Library browsing

Adding content

Deleting content

Citation & documents

Development

npm installnpm run build          # Compile TypeScriptnpm test               # Unit and per-tool tests (vitest, fetch faked, ~1000 tests)npm run test:e2e       # Built server over stdio against a local fake Zotero APInpm run smoke          # Quick stdio smoke test of the built server (user + group library)npm run bundle         # Claude Desktop extension: dist/mcp-zotero.mcpb (production dependencies only)npm run smoke -- --bundle dist/mcp-zotero.mcpb   # smoke test of the unpacked bundle, started from its manifestnpx tsx src/server.ts  # Run directly without building

Testing

Every test case is listed in test/TEST_CASES.md.

Live tests locally use only ZOTERO_TEST_* variables, never your ZOTERO_API_KEY:

ZOTERO_TEST_API_KEY=... ZOTERO_TEST_USER_ID=... [email protected] npm run test:live

Against a personal library add ZOTERO_LIVE_SAFE_MODE=1: the suite only creates items and collections named mzt-<runId>… and tagged mzt-run:<runId>, deletes only those, and skips collection deletion and group writes. A dedicated test account is marked by a collection named __mzt_disposable__.

Dependencies are updated monthly by a Claude Code agent (workflow, skill .claude/skills/deps-update); patch-only PRs are auto-merged after all required checks pass, anything else waits for review. GitHub Actions versions are updated by Dependabot.

CI setup (repository owner)

The agents authenticate to the Claude API with Anthropic Workload Identity Federation (GitHub OIDC, no API key). Recommended: one federation rule per environment, as narrow as possible:

Claims are exact-match string pairs (only subject_prefix supports a trailing *), so a prefix such as "this workflow on any ref" must be written as a CEL condition, as above; an exact job_workflow_ref (claude-deps, main only) can be a plain claim.

Audience https://api.anthropic.com. The subject is an exact match unless it ends with *; jobs that use an environment get the OIDC subject repo:Xevos117/mcp-zotero:environment:<environment>, so a rule written for a branch or PR subject never matches. Numeric ids (not names) keep a renamed or re-created repository/account from matching.

Trade-off for zotero-live: the "any ref" condition is needed for the agent smoke test to run on pull requests, but it also accepts a modified copy of that workflow file pushed to any branch of this repository (only people with write access can push). Pinning it to the exact claim job_workflow_ref: Xevos117/mcp-zotero/.github/workflows/claude-agent-smoke.yml@refs/heads/main closes that gap but disables the agent smoke test on PRs (it would then run only on manual runs from main).

Other owner settings:

• The Zotero test account needs a collection named __mzt_disposable__.
• Repository settings: "Allow auto-merge", and "Allow GitHub Actions to create and approve pull requests" (the dependency workflow opens its PR with GITHUB_TOKEN). Keep the ruleset at 0 required approvals: auto-merge of the dependency PR relies on it, and it is also what makes the second setting acceptable. That setting is a conscious trade-off: it lets workflows open PRs (needed) and approve them (not used by any workflow here); if approvals are ever required, it would let a workflow approve its own PR, so revisit it together with any approval requirement.
• No GitHub App is used by any workflow (the agents authenticate to Anthropic with Workload Identity Federation and use only GITHUB_TOKEN on GitHub, read-only for the agents). If the Claude GitHub App is installed on this repository, uninstall it.
• Set a monthly spend limit on the Anthropic workspace used by the federation rules: it is the real cap on agent costs.
• Residual risk: the agent smoke job that holds the OIDC token also runs the MCP server built from the PR's code (that is what it tests). It runs only for same-repository PRs by the owner or a bot, the token is bound to the zotero-live environment and the workspace spend limit caps any misuse.
• Required checks after the stack merges: test (node 22), test (node 24), test (node 26), live-tests, agent-smoke.

Releasing

1. Update CHANGELOG.md (move Unreleased to the new version) and the version in package.json, in server.json (version and packages[0].version) and in manifest.json (npm test fails if they differ).
2. Make sure CI, live tests and the agent smoke test are green on main.
3. Run the manual Word checklist on a document injected by the release candidate and record the results in its log.
4. Before the first release that ships the Claude Desktop extension (and whenever manifest.json or the Node.js requirement changes): build it with npm run bundle, install dist/mcp-zotero.mcpb once in a real Claude Desktop (macOS or Windows), fill in a test key and user ID, and check that the 15 tools appear and get_collections answers.
5. Publish the GitHub release: the release workflow runs the tests, publishes to npm, publishes server.json to the MCP Registry and attaches the skill zips and the Claude Desktop extension (mcp-zotero.mcpb). The release tag must be the version (e.g. 2.0.3): the registry and bundle jobs check out the tag and fail if package.json differs.
6. If only the mcp-registry job fails, use Re-run failed jobs on the run: Re-run all jobs stops at the npm publish (the version already exists) and so never reaches the registry.

Debug with MCP Inspector

npx @modelcontextprotocol/inspector npx tsx src/server.ts

License

MIT - see LICENSE for details.