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Mendeley vs Zotero: An Honest Comparison and Why I Ultimately Chose Zotero for My Thesis

Mendeley vs Zotero comparison: features, pros, cons, and why I switched to Zotero


Choosing the right reference manager can make or break your academic writing workflow. Whether you're writing journal articles, a thesis, a dissertation, or even a full-length book, tools like Mendeley and Zotero are often at the center of the decision.

In this article, I share a practical, experience-based comparison between Mendeley vs Zotero, along with the real reasons why I decided to switch from Mendeley to Zotero during my thesis journey.

What Attracted Me to Mendeley in the First Place?

Mendeley is widely known for its user-friendly interface and generous free cloud storage. When I first started writing academic papers, several features immediately caught my attention:

  • 2 GB of free cloud storage
  • Web-based version available
  • Desktop application support
  • Seamless PDF management
  • Integration with Microsoft Word

For someone who frequently stores books, journal articles, and reference files, the 2 GB free cloud storage felt like a huge advantage. The web version was also convenient—I could access my references from anywhere without always relying on my PC. Because of these strengths, I confidently chose Mendeley for writing journal articles—and later, for my thesis.

My Experience Using Mendeley for Journal Writing

When I used Mendeley for journal articles, everything worked smoothly. Both the web version and desktop application performed well. Citation insertion was fast, synchronization worked reliably, and I encountered minimal issues. At this stage, I had no reason to consider switching.

The Problems Began During My Thesis

However, things changed when I started working on my thesis—a much larger and more complex document. Here are the three major issues I experienced:

Performance Issues with Large Documents

I discovered that Mendeley struggles with large documents such as Theses, Dissertations, and Books. As my thesis grew longer and the number of citations increased, Mendeley became noticeably slower. Citation insertion took longer, and document processing lagged. For smaller projects, it works well. But for large-scale academic writing, performance becomes a serious concern.

Microsoft Office Integration Error (September 2025)

In September 2025, I encountered a frustrating issue: Mendeley’s integration with Microsoft Office stopped working for nearly a month due to an Office update. Microsoft Office had released an update, and Mendeley’s plugin became temporarily hung. For almost a month, I couldn’t insert citations properly. So, my writing process was interrupted, and finally, I chose to pause my thesis work. This was a turning point. Academic writing depends heavily on reliability. When your citation manager fails, your entire workflow collapses.

Citations Disappeared (December 2025)

The most serious issue occurred in December 2025. I normally worked on my thesis using Mendeley Desktop and Microsoft Office Desktop. One day, I tried using Microsoft Office Web and Mendeley Web. Everything seemed fine at first. But when I returned to the desktop version—all my citations were gone. At that moment, I asked myself: 

Is Mendeley truly reliable as my long-term academic writing partner?

Losing citations in a thesis is not a small issue. It costs time, energy, and emotional stability. After long consideration, I decided to switch.

Why I Switched to Zotero

Zotero is another popular reference management software, widely used in academic communities. Initially, I hesitated because Zotero’s free cloud storage is relatively small compared to Mendeley. However, I discovered something important.

Zotero + Cloud Storage = Powerful Combination

Although Zotero’s free storage is limited, you can integrate it with external cloud services like Google Drive, Dropbox, and OneDrive. With the help of plugins, Zotero can automatically sync PDF files to external cloud storage. I personally chose to integrate Zotero with OneDrive. Now, whenever I attach a file, it automatically syncs to OneDrive. This solution effectively removes Zotero’s storage limitation problem.

What Makes Zotero More Reliable?

After switching, I noticed several advantages:

Better Stability for Large Documents 

Zotero handles large thesis documents more smoothly.

Rich Plugin Ecosystem

Zotero has a massive community and many powerful plugins available online.

Open-Source Flexibility

Zotero is open-source, which means:

  • Faster community-driven updates
  • Greater transparency
  • More customization options
Smooth Performance

In my experience, Zotero feels lighter and more stable—especially for long academic writing projects.

Mendeley vs Zotero: Quick Comparison

Feature Mendeley Zotero
Free Storage 2 GB 300 MB
Web Version Yes Limited
Large Document Performance Slower More Stable
Plugin Ecosystem Limited Extensive
Open Source No Yes
External Cloud Integration Limited Easy via plugins

Final Verdict: Why I Chose Zotero

Mendeley is not a bad tool. In fact, it works very well for:

  • Journal articles
  • Small to medium projects
  • Users who prioritize built-in cloud storage

However, for long-term academic writing like a thesis, I need:

  • Stability
  • Reliability
  • Plugin flexibility
  • Cloud integration control

Zotero offers exactly that. Switching required effort—especially fixing the lost citations—but in the end, it was worth it.

Conclusion: Which One Should You Choose?

If you're writing short academic papers and want easy cloud storage, Mendeley may suit you. If you're working on:

  • A thesis
  • A dissertation
  • A book
  • Long-term academic projects

Zotero might be the safer and more reliable choice. Your reference manager is not just software—it’s your academic writing partner. Choose wisely.

If you're currently deciding between Mendeley vs Zotero, I hope this honest experience helps you make a better choice.