January 18, 2013

How to export, delete and move your Mendeley account and library #mendelete


Delete. Creative Commons licensed picture by Vitor Sá – Virgu via Flickr.com

News that Reed Elsevier is in talks to buy Mendeley.com will have many scientists reaching for their “delete account” button. Mendeley has built an impressive user-base of scientists and other academics since they started, but the possibility of an Elsevier takeover has worried some of its users. Elsevier has a strained relationship with some groups in the scientific community [1,2], so it will be interesting to see how this plays out.

If you’ve built a personal library of scientific papers in Mendeley, you won’t just want to delete all the data, you’ll need to export your library first, delete your account and then import it into a different tool.

Disclaimer: I’m not advocating that you delete your mendeley account (aka #mendelete), just that if you do decide to, here’s how to do it, and some alternatives to consider. Update April 2013, it wasn’t just a rumour.

Exporting your Mendeley library

Open up Mendeley Desktop, on the File menu select Export. You have a choice of three export formats:

  1. BibTeX (*.bib)
  2. RIS – Research Information Systems (*.ris)
  3. EndNote XML (*.xml)

It is probably best to create a backup in all three formats just in case as this will give you more options for importing into whatever you replace Mendeley with. Another possibility is to use the Mendeley API to export your data which will give you more control over how and what you export, or trawl through the Mendeley forums for alternatives. [update: see also comments below from William Gunn on exporting via your local SQLite cache]

Deleting your Mendeley account #mendelete

Login to Mendeley.com, click on the My Account button (top right), Select Account details from the drop down menu and scroll down to the bottom of the page and click on the link delete your account. You’ll be see a message We’re sorry you want to go, but if you must… which you can either cancel or select Delete my account and all my data. [update] To completely delete your account you’ll need to send an email to privacy at mendeley dot com. (Thanks P.Chris for pointing this out in the comments below)

Alternatives to Mendeley

Once you have exported your data, you’ll need an alternative to import your data into. Fortunately, there are quite a few to choose from [3], some of which are shown in the list below. This is not a comprehensive list, so please add suggestions below in the comments if I missed any obvious ones. Wikipedia has an extensive article which compares all the different reference management software which is quite handy (if slightly bewildering). Otherwise you might consider trying the following software:

One last alternative, if you are fed up with trying to manage all those clunky pdf files, you could just switch to Google Scholar which is getting better all the time. If you decide that Mendeley isn’t your cup of tea, now might be a good time to investigate some alternatives, there are plenty of good candidates to choose from. But beware, you may run from the arms of one large publisher (Elsevier) into the arms of another (Springer or Macmillan which own Papers and ReadCube respectively).


  1. Whitfield, J. (2012). Elsevier boycott gathers pace Nature DOI: 10.1038/nature.2012.10010
  2. Van Noorden, R. (2013). Mathematicians aim to take publishers out of publishing Nature DOI: 10.1038/nature.2013.12243
  3. Hull, D., Pettifer, S., & Kell, D. (2008). Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web PLoS Computational Biology, 4 (10) DOI: 10.1371/journal.pcbi.1000204
  4. Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2010). Utopia documents: linking scholarly literature with research data Bioinformatics, 26 (18) DOI: 10.1093/bioinformatics/btq383


  1. Note that clicking the Delete Account button will not delete all the data you entered into Mendeley. As detailed on Mendeley’s Privacy page , you will have to write an e-mail to privacy [at] mendeley [dot] com in order to make sure they delete all their copies:


    Generally, you can edit and delete any personal data you upload to our Site. If you wish to deactivate your account you may do so by sending a request to privacy [at] mendeley [dot] com. Removed information may persist in backup copies for a reasonable period of time and as necessary to comply with our legal obligations. However, please note that this information will not be generally available to other users or registered members.

    Non-personal information about research documents, such as bibliographic information, abstracts, keywords, or cited references will persist in our database and will not be deleted automatically when you deactivate your account, unless you specifically request this by contacting us at privacy [at] mendeley [dot] com. If non-personal information about research documents is in the public domain or has also been uploaded by other users, we may opt to retain it in our database to ensure continued service to these other users. Where you make use of the interactive features of the service to share information with other users and registered members (e.g. sending a personal message to another user) you may not be able to remove such communications.”

    Comment by P. Chris — January 18, 2013 @ 9:28 pm | Reply

    • Thanks for pointing this out, seems like the same kind of delete as a facebook “delete”…

      Comment by Duncan — January 21, 2013 @ 12:15 pm | Reply

  2. Hi, I’m from Mendeley. We have always given researchers control over their data. In addition to the availability of your library via export and the open API, your library is also stored locally in a open format called sqlite, which many applications can read and convert.

    We’ve always probably been about openness, no matter what rumors you may have heard.

    Comment by drgunn — January 19, 2013 @ 3:20 pm | Reply

    • Hi William, strictly speaking SQLite is a database not a format, but I’m nit-picking. It does provide another option for export which I didn’t know about, so thanks for commenting.

      Comment by Duncan — January 21, 2013 @ 1:25 pm | Reply

  3. Hi, I’m from Mendeley. In addition to export and the Open API, you data is stored locally in an open format called sqlite, which many programs can read and convert. We’ve always given researchers control over their data, no matter what rumors are circulating about us.

    Comment by drgunn — January 19, 2013 @ 3:23 pm | Reply

  4. Duncan, CiteULike isn’t owned by Springer but is privately owned. Springer did sponsor us for a couple of years, but that ended years ago.

    Comment by Fergus Gallagher — January 23, 2013 @ 9:56 am | Reply

    • Thanks Fergus, didn’t realise this…

      Comment by Duncan — January 23, 2013 @ 1:26 pm | Reply

      • Thanks for the edit – may I suggest a change to the last sentence as well? “(Springer or Macmillan which own Papers, Citeulike and ReadCube).”

        Comment by Fergus Gallagher — January 23, 2013 @ 3:36 pm

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  9. Thanks bro, I’ve switched to Zotero now. Open source & AGPL. Reasonable price for storage plans. You can also export all you Mendeley data to SQLite file from choosing Help -> Create Back up. The ZIP file contains SQLite databases. Be sure to select all (CTRL+A) before you do this, by default, if backs up only the *selected* items. So, select all first!

    Comment by Stochastic Matrix — April 10, 2013 @ 11:44 pm | Reply

  10. Qiqqa.com, a free reference and research manager, lets you import your PDFs, BibTeX, comments, tags and annotations.directly from Mendeley.

    Comment by Jimme — April 16, 2013 @ 12:31 am | Reply

  11. Stay classy, Jimme.

    Comment by drgunn — April 17, 2013 @ 6:39 pm | Reply

  12. […] weighed in on the matter (examples here and here). Good friend Duncan Hull has posted on his blog a step-by-step guide on how to delete your Mendeley account, which seems to be making the rounds on the blogosphere and the […]

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  13. The button of “export” in the file menu is not active in my computer… what is the solution?

    Comment by Hafiz kabeer raza — September 4, 2015 @ 6:05 pm | Reply

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