Switch from Mendeley to PapersFlow — Complete Migration Guide (2026)

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Frequently Asked Questions

Will I lose my Mendeley annotations when I switch?

Yes, annotations (highlights, sticky notes, margin comments) do not transfer via BibTeX export because Mendeley stores them in a proprietary format. Your paper metadata, titles, authors, DOIs, and folder organization all transfer cleanly. If your annotations are critical, you can keep Mendeley installed as a read-only archive while using PapersFlow for all new work. Over time, PapersFlow's AI analysis replaces much of the manual annotation workflow — instead of highlighting key findings yourself, the AI extracts them automatically.

Can I import my Mendeley groups and shared collections?

Mendeley Groups cannot be exported directly. However, you can export the papers in each group as separate BibTeX files and import them into shared PapersFlow projects. Ask group members to switch to PapersFlow's shared projects, which offer AI-powered collaboration that Mendeley Groups never provided — shared analysis, collaborative literature reviews, and team-wide counter-evidence search.

How do I replace the Mendeley Word plugin?

Connect PapersFlow to Zotero via bi-directional sync (free, takes 5 minutes). Install Zotero's Word plugin. Your PapersFlow library syncs to Zotero automatically, and Zotero's Word plugin handles citation insertion and bibliography generation. The workflow is nearly identical to Mendeley Cite, with access to 10,000+ CSL citation styles — more than Mendeley offers. Many researchers find Zotero's plugin more reliable than Mendeley's.

Is Mendeley desktop being discontinued?

Mendeley Desktop (the original desktop application) was officially discontinued in September 2022. Elsevier replaced it with Mendeley Reference Manager, a rebuilt web-based application with fewer features than the original desktop version. Many researchers have reported that the new version lacks features they relied on — particularly advanced annotation tools, folder management, and offline capabilities. This forced migration is one of the primary reasons researchers are looking for Mendeley alternatives.

Can I use both Mendeley and PapersFlow during the transition?

Absolutely. Import your Mendeley library into PapersFlow and use PapersFlow for AI analysis and new paper discovery while keeping Mendeley for any annotation workflows you're not ready to change. There's no conflict between the two tools. Many researchers run both for a few weeks before fully committing to PapersFlow. The key advantage is that your imported papers immediately gain AI analysis capabilities they never had in Mendeley.

How long does migration take?

For most researchers: under 15 minutes. Exporting from Mendeley takes 1-2 minutes. Importing to PapersFlow takes 1-2 minutes even for large libraries (500+ papers). Setting up Zotero sync adds 5 minutes if you need the Word plugin. The metadata resolution happens automatically in the background. Libraries with 1,000+ papers may take slightly longer for full metadata resolution, but you can start working immediately while it completes.

What about my Mendeley paper recommendations?

Mendeley's recommendation engine suggests papers based on your library and what other Mendeley users read. PapersFlow's discovery is more powerful: AI agents search across OpenAlex (250M+ works), Semantic Scholar, and Exa using semantic understanding, not just collaborative filtering. You get recommendations based on what your research actually needs, not what other people clicked on. The Deep Scan workflow can discover 50-100 relevant papers in a single automated run.

Is PapersFlow free like Mendeley?

Both have free tiers. Mendeley offers 2GB free storage with paid plans for more. PapersFlow's free tier includes core reference management, paper discovery, and basic AI features. PapersFlow Pro unlocks advanced multi-agent analysis, Deep Scan systematic reviews, and higher usage limits. For researchers switching from Mendeley's free tier, PapersFlow's free tier covers equivalent reference management plus AI capabilities Mendeley doesn't have at any price.

What if I have thousands of papers in Mendeley?

PapersFlow handles large library imports well. BibTeX files with 2,000+ entries import without issues. The metadata resolution (matching each reference to OpenAlex and Semantic Scholar records) runs in the background — you can start using your library immediately. Export from Mendeley in batches by collection if the full export is slow. Researchers with 5,000+ paper libraries have successfully migrated without data loss.

Does PapersFlow support Mendeley's BibTeX format specifically?

Yes. PapersFlow's BibTeX importer handles Mendeley-specific quirks automatically — including non-standard fields, escaped characters, and Mendeley's unique reference key format. You don't need to clean up the export file. Just export from Mendeley and import directly into PapersFlow.