Scrivener & Mendeley

Hi, I’ve just started a PhD, and have discovered Scrivener - which seems a real gem for the writing process. I’m a long time user of Mendeley which I am a big fan of - I really like its PDF reader, meta-data extraction and annotation features and cross platform capabilities (I use Mac & PC). In the past I have used Mendeley’s Cite-While-You-Write Word Plugin and this is by far the most important function of Mendeley I use.

Now it seems that Mendeley doesn’t have an equivalent CWYW plugin for Scrivener, nor any sort of RTF scan feature as other citation software does. I’ve read a few suggestions on here and elsewhere for workarounds but none have seemed great: Pasting Formatted citations into Scrivener from Mendeley seems impractical for a 80,000+ word thesis and it is not the convention in my area (health sciences) to use footnotes for references, just an intext (Smith et al., 2013) and a long bibliography.

Has anyone found a good solution for getting the benefits of both Mendeley & Scrivener? Has anyone found a good workflow using these tools - and is it necessary to bring in an extra piece of software into the mix like zotero or papers?

Any suggestions would be appreciated…

Before I say anything more, I want to be upfront in acknowledging I haven’t used Mendeley. However, I wrote my doctoral thesis in Scrivener, and in a field that required parenthetical author-date citations (specifically, APA style). While I used EndNote for my bibliography, I didn’t find copy’n’paste (or drag’n’drop) to be too impractical. Further, once I got going, I was able to manually enter many of the citations. And when I was really gunning it with writing and didn’t want to lose the flow, I’d simply use Scriveners inline annotation feature to insert a comment reminding me to insert the relevant citation with something like “citation for Bloggs and Smith, 1887 or 1903 or whenever it was”. Later, on the days when I couldn’t write to save myself, I could go through and copy’n’paste (or drag’n’drop) at my leisure, confident in the knowledge I was still doing something important and making progress on my thesis. This had the added benefit of causing me to reread, and often edit, those sections. Always helpful with a thesis.

That’s for the writing aspect. For preparing for publication, you are better off compiling to Word and using Mendeley’s Word features. But even without Mendeley, you would be better off compiling to Word for final layout and copy-proofing, so this isn’t much of a loss, if any.

Of course, all the above is predicated on the assumption that Mendeley operates in a similar way to EndNote and Papers, etc. If not, see my opening sentence…

Thanks for the response nom (I must confess to have not used Endnote in a long time following a string of bad experiences) - Just to clarify, When I say pasting the formatted citations from Mendeley: What this does is that it copies the long bibliographic entry that would normally go at the end with all the journal details etc. Rather than the intext (Smith et al., 2013) bit. Suggestions on how to use this have focused on having a separate scrivener ‘chunk’ to which you paste citations as you go along, but I felt this was rather cumbersome and could easily get muddled as I add/take away references as I go along.

I don’t know if this is the same as the drag and drop in endnote - or whether that gives you a nice intext citation and then allows you to create a bibliography?

Anyway my plan is eventually to compile everything to word as and when thats needed - but I wasn’t sure if going through at that point and then inserting references was that great a plan either - its a possibility but wondered if there were other solutions (the idea of compiling the whole document at the end and adding in references fills me with fear!).

Drag’n’drop / copy’n’paste from EndNote results in a temporary in-text citation that looks like this {Nadkarni, 2012 #1714} (note that this is a real EndNote citation that I just dropped this text box).
In Papers, you choose in preferences whether it will insert a temporary citation like {Nadkarni:2012eg} or the full reference (see below for the full reference). After you complete your paper/thesis/article/academic-masterpiece, you compile to Word (or other word processor) and then use the relevant software plug-in to convert the temporary citations to properly formatted citations and the reference list.

Does Mendeley have a similar feature?

UPDATE: I’ve just watched a short video on Mendeley here. It looks like Mendeley attempts to create the “proper” citation first go, which means that (a) you can’t tell which citations were added by Mendeley and which were added by you and (b) could prove troubling if you add more references later.

If you want a similar feel to the pop-up window option that Mendeley uses, try Papers 2 as it offers something similar that does work with Scrivener. Papers has come a long way and seems to offer most, if not everything, that Mendeley does. Although not free, it does have an academic price which seems reasonable (I bought it when a student, and paid for the upgrade a few years later - if the upgrade had come 12 months earlier, I may not have used EndNote at all).

I have a love-hate relationship with EndNote. I love the fact that my university offers it for free. :wink:
Actually, EndNote has also improved dramatically. While it is still ugly and, at times, confusing, it is much more stable than it used to be. Also, it is mega-powerful compared to Papers (or any of the other reference manager apps I’ve investigated over the years). Because of its power, I was able to edit its templates to correct some minor errors in the way it implemented APA style (actually, I edited an edited version of the template I found from a New Zealand university). Note, however, that I don’t use EndNote’s cite-while-you-write feature in Word; that just seems to be a recipe for pain and distress, which is also why I didn’t like the video demo of Mendeley. That approach seems fine for short works but not, to my mind, pieces that are tens of thousands of words long.

If you like editing under the hood, EndNote is good. If you like simple and understandable, I think Papers is awesome and worth investigating. Phrased in a way that does not favour any individual reference manager, if I had to choose between my reference manager of choice or Scrivener, I’d swap my reference manager without question.

Nadkarni, A., & Hofmann, S. G. (2012). Why do people use Facebook? Personality and Individual Differences, 52(3), 243–249. doi:10.1016/j.paid.2011.11.007

Thanks nom, great response. I’ve been looking at papers actually, seems a good alternative - I might try the trial version and see how I get on. My Uni also has an endnote subscription - although I’m not sure which version - people keep telling me its got better but once burnt…

Good to hear that you think Scrivener is worth the hassle of changing reference managers - it seems to have such great features that I’m determined to use it as much as possible - getting out of the habit of using Word will be interesting!

Good luck. Post back to let us all know how you got on. I’m sure you’re not the only one grappling with reference managers and theses…

Caveats: I am a BA student, not Ph.D., I use a Mac exclusively (but have access to Windows), use Papers 2 for Mac, and Scrivener, all for writing my multiple papers.

I actually used Mendeley for Mac before I bought Papers, and found Paper 2 (free trial available) to be much improved over Mendeley for flexibility and ease of use. Papers has “Citations” as a menu-bar applet and plug in for the major browsers, that does a good job of letting me cite into Scrivener or Word:Mac 2011.

Scrivener is where I write the main parts of my text, then compile to Word (.docx) for final layout/editing/submission. Once I compile from Scrivener to Word, I can use Papers 2 “Citations” hotkey to have it format the citations and attach the citations/references to the end of the document.

Like nom said, let us know how you get on! I’m interested to hear your experience with this workflow.

I’m bumping this up because I’d like to enlist more support in getting Scrivener integration on Mendeley’s agenda. I also thought I would share my workflow workaround to see whether Scrivener users have any additional thoughts.

If you are also a Mendeley user, please let them know how important Scrivener integration is to you by adding your vote to the Mendeley feedback page:

Since I, too, use author-date format for citations, my Mendeley workaround has been to insert these manually–Not too hard to simply type (Smith 2014). I then use Scrivener’s commenting feature to copy/paste (or simply drag and drop) the associated reference from Mendeley into a Scrivener comment. This is for my own use so that I always know exactly what (Smith 2014) is. If I later choose to delete the citation in my revisions, the comment gets deleted as well. So at any stage in the process, I can click on my draft folder and see (in the comments pane) all the references that are currently in my draft. (I should say that I rarely use comments for other purposes, so this works well for me).

When it comes time to assemble a bibliography or reference list, I go to the folder I have assigned in Mendeley for this project. If doing a bibliography (i.e. a list of all relevant works consulted in the project, whether or not specifically cited in the text), this is extraordinarily easy. Simply “select all” from the relevant Mendeley folder and copy/paste (or drag/drop) the citations over to the bibliography document in Scrivener. (For some bizarre reason, they will be in 12 pt. Times New Roman, but the font can be easily fixed). In less than 5 seconds, a nicely formatted bibliography.

In the more common scenario where one wants only “References” (i.e. works directly cited in the text), it takes a bit more work. I would print out a full bibliography (from an ordinary text or Word file) from Mendeley using the “select all” method above. Then I would scroll through my Scrivener comments pane checking off on my printout which references I need to drag/drop into my Scrivener references document. Although it’s not automated, in a typical 30-page paper, I imagine one could do this in about 10 minutes. (A thesis or dissertation is obviously a more complicated situation although not impossible).

The only major pitfall in this workflow is if one discovers that there are multiple (Smith 2014) works cited, such that one should be using (Smith 2014a), (Smith 2014b), etc., for the inline citations. This should be immediate evident from the final reference list though, in which case one could easily use Scrivener’s search function and manually correct the relevant citations.

For a dissertation or book-length manuscript, another alternative would be to use Scrivener in conjunction with LaTex, in which case one would use BibTex for citation management. Mendeley will sync with BibTex, which is what I suspect most of their core users in the sciences are doing. Still, there’s a an important role for Scrivener integration for those who do need to work at times in other formats besides LaTex.

Anyway, these are my initial thoughts on how I might best use Scrivener and Mendeley together. If any one has more efficient solutions, I would love to hear them.

Hi Guys. I guess you have successfully finished your PhD and move forward to the next stage of your career. Thanks very much for sharing your experiences and insights on using Scrivener with Mendeley. It is very helpful, and answers a lot of my questions.

I just started using Scrivener and find it could be really useful when writing first draft. A problem I have observed (correct me if I am wrong): when importing Mendeley referenced text from Word to Scrivener, the linkage is not kept (- this should be ture, otherwise there is Mendeley support in Scrivener). And when the same text are copied back to word from Scivener, the Mendeley style in text reference can no longer be recognized by Mendeley.

Although the support for Mendeley citation is not available at the moment. The usefulness is more than the this little inconvenience for me.

To do referencing in Scrivener, I am thinking to create a footnote or comment (or inline annotation or inline comment), with information on the paper name, also some extra comment. The reference can be added at last when the Thesis is almost done. Similar to the way described here :

This is based on the user case of using Scrivener as a 1st draft tool for Thesis. With this said, I do hope to see the integration on Mendeley with Scrivener. (But I guess it could be a lot of development work, as different software platforms have different goals to optimize and philosophy behind them, which may not be compatable.)
Will see


Since Elsevier bought Mendeley, I don’t think one can expect them to integrate with anything beyond Word, unfortunately. The big journal publishers have little incentive to innovate.

I think the best option is for Scrivener to integrate citeproc as described in this thread:


Please add a note if that’s an option that would work for you.

I think your best option is to stick with Endnote as you can easily make the citation format yourself and there is no confusion that seems to happen with Mendeley. Most of my doc students use Mendeley because it is free, but I find Endnote to be superior enough (due to the ability to search through all the pdf text of the articles I attach to each entry) to be worth the cost. Try the demo of Endnote to get a feel if it will work for you. The import/export of both will make giving one a trial and moving back, if need be, simple.

I think Mendeley is a strong second option and likely to be a first option if they continue to improve and offer free software. I like Mendeley’s look, but love PDF searching. You will use the software forever, so the cost of Endnote is not a big deal.

I use Scrivener and Endnote for journal publications and a research methodology text I am writing. I would love to see a plugin for either that let you cite while you write as you can in Word.