Zotero vs Mendeley vs EndNote (2025)
The definitive comparison of reference managers for researchers. Find the best tool for managing your citations.
Last updated: December 2024 | Reading time: 12 minutes
TL;DR - Quick Recommendations
- Zotero:Best free option. Open source, works everywhere, active community. Choose this unless you have a specific reason not to.
- Mendeley:Best for discovery/social features. Nice UI, but owned by Elsevier (privacy concerns).
- EndNote:Best for institutions. Expensive but powerful. Use if your university provides a license.
Reference Manager Overview
Free (300MB) / $20-120/year storage
Pros
- Completely free for core features
- Open source - no vendor lock-in
- Best browser extension for capturing
- Works with any word processor
- Active community & plugins
- Self-hosting option available
Cons
- Limited free cloud storage (300MB)
- UI feels dated compared to Mendeley
- PDF reader less polished
- No built-in social/discovery features
Free (2GB) / $55-165/year premium
Pros
- Generous free storage (2GB)
- Sleek, modern interface
- Built-in PDF reader with annotations
- Social networking features
- Mendeley Suggest for discovery
- Good iOS/Android apps
Cons
- Owned by Elsevier (privacy concerns)
- Limited export options
- Desktop app discontinued in favor of web
- Less reliable browser extension
- Sync issues reported by users
$275 one-time / $175/year subscription
Pros
- Industry standard in many institutions
- Powerful for large libraries (50k+ refs)
- Excellent Word integration
- Strong customer support
- Often included in institutional licenses
- Most citation styles available
Cons
- Very expensive for individuals
- Steep learning curve
- Outdated interface design
- No free tier
- Syncing can be slow
- Overkill for small projects
Feature Comparison
| Feature | Zotero | Mendeley | EndNote |
|---|---|---|---|
| Price | Free | Free | $275+ |
| Free Storage | 300 MB | 2 GB | None |
| Open Source | Yes | No | No |
| Browser Extension | Excellent | Good | Good |
| Word Plugin | Yes | Yes | Excellent |
| Google Docs | Yes | Limited | Yes |
| PDF Annotation | Basic | Good | Good |
| Mobile Apps | iOS/Android | iOS/Android | iOS |
| Collaboration | Groups | Groups | Share libraries |
| Offline Access | Full | Limited | Full |
| Learning Curve | Easy | Easy | Steep |
| Citation Styles | 10,000+ | 8,000+ | 7,000+ |
Recommendations by Use Case
Free, easy to learn, works with any word processor. Perfect for dissertations.
Good discovery features, social networking, nice PDF reader for literature reviews.
EndNote if institutional license available; Zotero otherwise. Both handle PubMed well.
Best for managing 50k+ references with multiple collaborators.
Open source, can self-host, no corporate data harvesting.
Zotero exports clean BibTeX that imports directly into TypeTeX. Best of both worlds.
Privacy & Data Ownership
Best for privacy. Open source, non-profit, can self-host. Your data stays yours. No tracking or analytics beyond basic usage.
Privacy concerns. Owned by Elsevier. Your reading habits and library data may be used for analytics. Read their privacy policy carefully.
Commercial but established. Owned by Clarivate. Standard commercial data practices. Desktop version keeps data local.
Frequently Asked Questions
Yes. Export your Mendeley library as BibTeX or RIS, then import into Zotero. PDFs need to be re-added or migrated separately. There are community guides for migrating annotations.
Core features are 100% free forever (open source). You only pay for cloud storage beyond 300MB. You can also use your own WebDAV server for unlimited free storage.
Historical reasons - EndNote has been around since 1988. Many institutions have site licenses making it "free" for users. It's deeply integrated into many academic workflows.
Papers (now ReadCube Papers) is good for Mac users ($3/month). Paperpile is excellent for Google Docs users ($3/month). Both are solid alternatives worth considering.
All three support collaboration, but differently. Zotero Groups are free and unlimited. Mendeley Groups are free up to 3 people. EndNote requires everyone to have a license.
Mendeley has Mendeley Suggest for paper recommendations. Zotero has community plugins for AI integration. EndNote recently added some AI features. For AI-powered citation suggestions, TypeTeX offers this natively.
Using Reference Managers with TypeTeX
All three reference managers export to BibTeX, which TypeTeX imports directly:
- Zotero + Better BibTeX: Best integration. Auto-syncs your library with TypeTeX
- Mendeley: Export as BibTeX and import into TypeTeX
- EndNote: Export as BibTeX (may need cleanup) and import
- TypeTeX Native: AI-powered citation suggestions without external tools
Related Citation Guides
Skip the reference manager complexity
TypeTeX has built-in citation management with AI-powered suggestions. Import your existing BibTeX library or start fresh - no external tools required.
Try TypeTeX FreeThis comparison is based on publicly available information as of December 2024. Prices and features may change. We are not affiliated with Zotero, Mendeley, or EndNote. TypeTeX is a separate product.