Reference managers: Migrating from Mendeley to Zotero

Today is Software Freedom Day and I thought it would be the perfect time to talk about a software migration I am currently making. I started using Mendeley back in my honours year and was happy enough with it to make a very positive blog post about it in 2012. I was less happy when it joined with Elsevier but continued to use it nonetheless. Now, I am switching to use Zotero as my reference manager in the future. Why?

It’s complicated and there isn’t just one specific reason. I have been uncomfortable with the association between Elsevier and Mendeley for several years. As I wrote earlier this year, I think we should use free software when possible; Mendeley is not, Zotero is. I’ve also seen that Mendeley is moving away from its current desktop manager to a new reference manager which is cloud-based. I am not a fan of cloud-based programmes because it leads to a huge loss of control of your data (Mendeley already encrypts your database on your own computer which makes migrating more difficult.) and what you can do with a particular programme. That’s perhaps even a bit hypocritical because I am paying for storage on Mendeley server’s to sync my library. But I almost never actually need that and I can do my own backups for free. Lastly, after a recent update of LibreOffice, I found that Mendeley was no longer able to create citations. That might not be their fault but all these little things start to add up.

I have been using Zotero for just over two weeks now and thought I should reflect on some of my experiences, particularly how it compares to Mendeley. I did look at it once near the beginning of the year and was not particularly impressed. It seemed functional but lacking in comparison with Mendeley, which I am quite comfortable with and like the way that it works.


  • Zotero doesn’t require you to make an account unless you want to use the sync feature. Mendeley required you to have an account to use it at all.
  • Zotero marks retracted items in your library! I saw this happen when importing my old papers and was pleasantly surprised as it’s something that Mendeley doesn’t do and something which I said should happen in my SAJS commentary.
  • It’s easy to rename files when there are multiple files. As far as I know, Mendeley didn’t allow that which made things very difficult if you had multiple supplementary files.
Comparison of how Mendeley (Red) and Zotero (Blue) treat multiple files for the same entry.
  • It’s really easy to add new items which I now have started doing with the DOI (In Mendeley I used to download the pdfs and add them into Mendeley). Zotero will even find the pdf for you, although that seems to work about as often as not.


  • Zotero opens PDFs with an external reader while Mendeley has a built-in PDF reader. The intention is to give you more choice over what you use to open articles with but it tends to just make things more cluttered; instead of six open articles in one Zotero window, you have an open Zotero window plus six other windows. It also means that, although Zotero lets you make notes on each article, any notes or highlights made on the pdf itself, is not indexed by Zotero. It’s only something I occasionally used but it’s quite annoying.
  • Although Zotero will create a citation from a DOI, it will not use a DOI to update an existing citation. This is why I stopped using the PDF import because in Mendeley I could import and then update by DOI if the information was wrong. In Zotero, I would have to create a whole new item and then merge it with the old entry.
  • Possibly linked to Zotero not opening PDFs internally but there is no automatic read/unread marker like in Mendeley. I collect a lot more articles than I read and knowing what I have and haven’t read is essential for managing the collection. In Mendeley that is very clear but in Zotero you have to individually add an “unread” tag to each article.
  • While Zotero does manage your folders, it does so in a way which is not human readable which makes finding files more difficult if you want to copy or share them. Mendeley had an easy-to-read and customisable folder structure.
Folder naming in Mendeley (top) versus Zotero (bottom).
  • Even without as many built-in features, it uses more memory. If I start both Mendeley and Zotero, I see Zotero using ~195 Mb of RAM versus Mendeley’s ~80 Mb.
  • There is no mobile version which can be a bit annoying if you want to easily transfer your reading to a tablet.

Overall, Zotero is not as nice to use as Mendeley and there are currently more negatives than positives on my list. Hopefully, over time and as I become familiar with Zotero, I will either get used to its quirks or find work arounds. But I guess I will take these small inconveniences in return for free (libre) software, more control over my own data and the opportunity to be free of Elsevier.


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