Foundation: Zotero Reference Management
Install and configure Zotero with Better BibTeX for free, powerful reference management
Why Zotero?
Zotero is the gold standard for free reference management:
- Open-source - Developed by the Corporation for Digital Scholarship
- 300MB free cloud storage + unlimited local storage
- 10,000+ citation styles - APA, MLA, Chicago, IEEE, and more
- Browser connector - One-click saves from any academic website
- Active plugin ecosystem - Extends functionality infinitely
- Better than paid alternatives - Outperforms Mendeley and EndNote
Installation
Install via Homebrew:
brew install --cask zoteroLaunch from Applications folder or Spotlight.
Install via package manager:
sudo apt install zoteroLaunch from application menu or terminal: zotero
Download installer from zotero.org/download
Run the installer and follow setup wizard.
Launch from Start menu.
Essential Plugins
1. Better BibTeX (REQUIRED)
Better BibTeX creates stable citation keys for Markdown/Pandoc workflows.
Why Better BibTeX? Zotero's default citation keys change when you edit metadata. Better BibTeX creates stable keys like smith_2024 that never change - essential for Markdown-based writing workflows.
Download Better BibTeX
Visit retorque.re/zotero-better-bibtex and download the latest .xpi file.
Save to your Downloads folder.
Install Plugin
In Zotero:
- Click Tools → Add-ons
- Click the gear icon (⚙️) → Install Add-on From File...
- Select the downloaded
.xpifile - Click Install Now
- Restart Zotero
Configure Citation Key Format
After restart, configure citation keys:
- Edit → Preferences → Better BibTeX → Citation Keys
- Set Citation key format to:
[auth:lower]_[year]
This creates clean citation keys:
- Single author:
smith_2024 - Multiple authors:
jones_martinez_2023 - Same author, same year:
smith_2024a,smith_2024b
Set Up Auto-Export
This is the magic that connects Zotero to everything else:
- Right-click My Library in left sidebar
- Select Export Library...
- Choose format: Better BibLaTeX
- Check ✓ Keep Updated
- Save to:
~/Documents/library.bib
Now your BibTeX file auto-updates whenever you add or edit references. No manual exports ever again.
Auto-Export Magic: The library.bib file now updates automatically. Point Pandoc, Obsidian, VS Code, or any Markdown editor to this file for instant citation access. Add a paper in Zotero → cite it immediately in your writing.
2. Zotero Connector (Browser Extension)
The browser connector is your one-click paper import tool.
Install Browser Extension
Visit zotero.org/download
Click the installer for your browser:
- Chrome / Edge / Brave
- Firefox
- Safari
Follow browser prompts to add extension.
Test the Connector
- Open Zotero desktop app (must be running)
- Visit any paper on Google Scholar, PubMed, or arXiv
- Click the Zotero icon in browser toolbar
- Paper + PDF automatically saved with metadata
Takes 2 seconds. No manual data entry ever again.
Verification Checklist
Confirm your setup is complete:
- Zotero desktop app installed and running
- Better BibTeX plugin installed and configured
- Citation key format set to
[auth:lower]_[year] - Auto-export configured to
~/Documents/library.bib - Browser connector installed
- Test import: Save one paper from Google Scholar
Next Steps
With Zotero configured, you now have:
- Automatic reference collection from any website
- Stable citation keys for Markdown writing
- Auto-updating BibTeX file for all your tools
Next chapter: Configure Obsidian to use your Zotero library for seamless note-taking and citation insertion.