This was a somewhat inevitable transition given my recent focus on privacy, data governance, sharing and the want for local control and access. I didn’t mind the removal of the social networking aspect of Mendeley, but the demise of the mobile app was too great of an impact on my workflow to continue using Mendeley. Yes, I could use the web app, but it’s clunky on tablet and I don’t always have internet access (reading papers by the lake, or on the train anyone?). I used Mendeley almost daily on my tablet to read papers that I synced from the desktop. I have NEVER used the web interface, and never will now.

Mendeley have sadly locked down the ability to import your library straight into Zotero, so there’s a bit of work involved, moreso if you have a large library. Mine involved a mix of exporting PDFs with annotations (only for papers I have a lot of notes taken on), and exporting folders as a bib file for import into Zotero as a new collection (which I then renamed to match the old folder name in Mendeley). I remember going through a similar pain when I switched from EndNote to Mendeley back in 2014, and I hope to not have to do this again for a long time.

I spent a few hours, and paid the $20 to get 2GB of cloud storage with Zotero. I figure that’s the same space I had with Mendeley, and I wasn’t using all of it having trimmed back my library a few years ago. I installed the Zoo for Zotero app (free) to access my library, and Xodo PDF reader (free) which plays nicely with Zoo for Zotero, and allows two-way syncing of PDF annotations. I also installed Zotfile add-in for Zotero which has this same sync functionality for other readers, and also gives you some control over file naming etc.

And now, I have a desktop app that has an MS Word citation plugin, 2GB cloud storage that syncs to a mobile app and permanent PDF annotations (Zotero uses a system PDF reader, Mendeley stores them separately). There is also an official iOS app in testing as I write.

Zotero isn’t perfect mind – I’ll miss the ability to have a watched folder for example. In order to continue my workflow for reading on tablet, which has become such an essential part of my process, I can live with that.

Bonus: Zotero can integrate with Scrivener for citation input as outlined here: – I’m looking forward to testing this ability in the future.

4 thoughts on “Goodbye Mendeley, Hello Zotero!

  1. I am probably a step behind you. I struggle with two things. I really like the Mendeley watched folder. And I have way too many folders in Mendeley. The loss of the iOS app was irritating, but I did nit find it very user friendly, so did not use it much. What to do! Zotero is on my list…

  2. I can’t argue with your logic Alan. I am a huge huge Mendeley fan, but no longer being able to read PDF’s in a native app is very limiting.

    I have been looking at options and may need to look more seriously at Zotero. Thanks for posting this piece. It was helpful.

  3. Hi!! I am a Mac user and have been desperately trying to figure out a workflow for PDF annotation and organization. Zoo isn’t available for Mac, as far as I can tell. What is it’s specific functionality? Can one use Xodo with Zotero alone? Would SO appreciate advice on how to set up a functional workflow for my research! Thank you!

    1. Hi Sabrina. I think you could use Xodo – I don’t use a Mac though. Zoo allows access to your library and folders in Zotero storage. I believe there are other apps that can do similar (or Zotero Web may work for you – a colleague recently tested this and was able to save annotations locally and to a shared library from an iPad), but I haven’t tried any others.

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