Best Reference Managers for Annotations and Note-Taking: What Reddit Users Really Think

Finding the right reference manager can make or break your research workflow. With so many options available, it's hard to know which one actually works for real people doing real research.

We dug through Reddit discussions to see what researchers and students are saying about popular reference managers. Here's what we found about the tools that people actually use every day.

Why Mendeley Falls Short for Most Users

Mendeley used to be a favorite, but Reddit users aren't happy anymore. The biggest complaint? Your annotations get trapped in the app itself.

One frustrated user explained that sharing annotated papers becomes a nightmare. When you highlight and add notes to a PDF in Mendeley, those annotations stay locked in the program. You can't easily share them with colleagues or move them to other tools.

The search function also disappoints users. The desktop version used to let you filter searches by author, year, or title. But the newer version stripped away these helpful features. Honestly, we personally do not know why they did this. Why take out something that your user like?

Many researchers have simply given up on Mendeley altogether. The program feels clunky and outdated compared to newer options.

Zotero Wins for Flexibility and Integration

Zotero consistently gets praise from Reddit users. The main reason? It plays well with other tools that researchers actually want to use.

Users love how Zotero lets them export annotations to note-taking apps like Obsidian. This creates a smooth workflow where you can annotate PDFs in Zotero, then organize those notes however you want in your preferred system.

The PDF management features also impress users. Zotero can automatically rename files, extract highlighted text, and keep everything organized. With extensions like Zotfile, you can set up rules that handle the boring file management tasks for you.

Cloud syncing works smoothly too. Users report that their references sync across all their devices without problems. Whether you're working on your laptop at home or a desktop at the office, your research stays up to date.

EndNote: Expensive and Complicated

Most Reddit users skip EndNote entirely. Even when universities provide it for free, people find it more trouble than it's worth.

The interface feels outdated and overly complex for basic tasks. Free alternatives like Zotero offer the same features with better user experiences.

Unless you're required to use EndNote for a specific project, most users recommend looking elsewhere.

Other Tools Worth Considering

Making Your Choice

The best reference manager depends on your specific needs. If you want something that works with other tools and gives you control over your data, Zotero consistently wins. For visual learners who like mapping connections, Liquidtext might be worth trying.

Remember that you can always switch tools later. Start with a free option like Zotero to test your workflow, then adjust as needed. The most important thing is finding a system you'll actually use consistently.

New Kid in the Block

Eaglecite is a modern reference manager built for researchers who need to find their citations fast. Our AI Search feature lets you search your library using natural language instead of hunting for exact keywords.

Instead of typing fragmented keywords like "elderly assistive technology statistics," you can simply ask: "What studies show statistics about older adults using assistive technology?" Eaglecite's AI instantly scans your entire citation library and surfaces the most relevant papers.

Beyond smart search, you get all the organization tools you expect like folders, tags, and sorting options to keep your references neat and accessible. But unlike clunky traditional software, everything works intuitively.