Struggling to move everything from Mendeley to Zotero

edited August 22, 2018
Hi, I want to move all my references from Mendeley to Zotero but I'm struggling to find a way to do it without losing data (including my PDF highlights!)

I downgraded Mendeley to use the direct importer ( but this doesn't preserve my PDF highlights.

I've seen mentions of Adios Mendeley ( which seems like it should work, or even just using Menextract2pdf after the direct importer ( But my technical knowledge isn't good enough to get the R script to work or figure out how else to do it?

Is there an idiots guide somewhere to completely moving over?
  • The direct importer should preserve the highlights (that's the main reason for its existence). What exactly are the steps you are taking to import with the direct importer. (Adios Mendeley is obsoleted by the direct importer.)
  • edited August 22, 2018
    No, the direct importer won't preserve PDF highlights, only PDF annotations. Mendeley stores highlights and annotations in its own database rather than in the PDF file itself, so the only way to move them elsewhere is by rebuilding the PDF, which would be very complicated. (The highlights are just pixel offsets in the database, not text.) So the Zotero importer will put the annotations into child notes with links to the PDF page, but not highlights.

    Mendeley can export PDFs with annotations and highlights, but only one file at a time (which is ridiculous). So if you really want to keep highlights for certain files, you can export those from Mendeley and then replace the PDF in Zotero with that one. To export in Mendeley, open the open the PDF and use File → "Export PDFs with Annotations…". To find the file in Zotero, right-click on the attachment and choose "Show File".

    (When you annotate files in Zotero you do so with a PDF reader of your choice, so you can choose how you want annotations and highlights to be stored. Most tools put them back in the same file, which is the best way to make sure they can be moved to another tool and also allows Zotero to sync them.)
  • (Sorry for misunderstanding what the issue was.)
  • The menextract2pdf programme seems to allow a bulk export of PDFs with highlights from Mendeley. If I do this for my whole library, what's the quickest way of matching those files with the zotero entries exported from Mendeley? Is zotero smart enough to match the PDF with the respective entry or am I still going to have to manually add each PDF to the right entry?
  • If I'm understanding that correctly, it writes the annotations and highlights back to the original PDFs in Mendeley, so if you run it before importing into Zotero, Zotero will import the PDFs with annotations and highlights.

    If you've already imported to Zotero and don't want to wipe everything and do it again, you could probably delete only the PDFs from Zotero and reimport, and Zotero will import just those missing items. You can do a search for "PDF" in All Fields & Tags mode in the middle pane, do a Select All to select only matching items, and then delete them and empty the trash.. It's possible you'd need to deselect a few matching items if "PDF" is mentioned in another field.
  • edited October 4, 2018
    Same here, there doesn't seem to exist a clear set of instructions for people who know neither how to use Github nor Phyton. A simple step by step description would be very helpful. I only got to download a zip file with the Github's Menextract2pdf package. Now what? How do I "run" this?

    Any help greatly appreciated.
  • Do you have python installed and running? I know that's a broad question, but we really can't provide support for python installs. Once that's the case (and make sure it's python 2.7, not the current 3.x version), let us know and we can walk you through the rest.
  • Thanks @adamsmith I have installed phyton 2.7.15. Now what? I am not even being able to load the Menextract2pdf package :(

    Thanks! Daniel.
  • what operating system?
  • edited October 4, 2018
    OK, that'll take me some time to write up reasonably. On Mac&Linux this is basically a one-liner, but Windows requires a good bit of set-up for running python.

    (If you do want to explore how to do this, start here: )
  • Sorry about that. And thanks a lot @adamsmith ! Daniel.
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