Zotero + Scrivener - What am I missing here?

Hi everyone, newbie poster here.

I’m an academic and I’d like to use Scrivener for my next book. I’ve read a lot on this forum (and others) about integrating reference manager software with Scrivener. I was a longtime user of Sente (RIP, sigh) and since it died I have played around with a lot of different managers (Mendeley, ReadCube, Papers2, Zotero, Bookends, Papers3) I’m not particularly happy with any of them. (Papers2 is dead, sigh, Papers3 is going to turn into a rental model - a big no thanks there - and I’m having a nightmare with Bookends trying to import content directly from a web browser vs. content from library or article databases through the program’s software.)

Zotero seems to be the best reference manager, at least for my field, but as far as I can tell, most users seem to think you need a computer programming degree to use it with Scrivener. (“Damnit, Jim, I’m a historian, not a software engineer!”)

That said, I’m starting to feel kinda crazy. I think maybe I’m missing something critical - because it doesn’t seem like it has to be that complex to me. Clearly, I’m doing something wrong.

SO, those of you using Zotero, can you help me out? Here’s what I’m doing. When I’m writing in Scrivener, I’ve designated Zotero as my citation manager. I insert a footnote, and in Scrivener hit command-y. It pops me over to Zotero. There, I just select the reference I want, hit command-shift-A to the citation from Zotero and then hop back to Scrivener and paste it into the footnote. Then, to ensure I don’t forget this source when I generate a bibliography later, I transfer that reference to a separate folder in Zotero labeled “bibliography” so that I know later to include it when I generate the bibliography.

What am I missing? Do I really need all very complicated (to me) computer programmy workarounds?

Thanks, everyone!

If you’re happy to manually keep the things you cite in Scrivener and your master Zotero list in sync as you add and remove refs manually, then your existing workflow should be fine. The potential problems with Zotero only come when you want to use temporary citations that will be scanned to automatically build the final bibliography. This is not really a problem with small numbers of refs, but as you get into the hundreds then automatic generation is worth the extra effort…

BTW if you have problems with Bookends import, post a message on their forums, you will usually get an immediate reply from the developer. Many refugees have come from Sente, so that route should not be problematic and easy to find a fix for…

Another vote for Bookends. I’ve used most of them, and paid for several of them. The one that keeps chugging along, reliably, and never going away, is Bookends. It has a developer who will actually reply to questions, and will solve problems where possible. He also notices when JSTOR, Google Scholar or others change their protocols and changes the program to keep up.

The program has a lot of power, which means complexity, but you don’t have to use it all. I’m a historian and psychologist, I’m 66 and no computer scientist, but I get it to do enough for me. Online search is not the best feature of the program, but on the other hand it will format bibliographies correctly, which some programs claim to do, but in fact do not.

One of the problems in adapting to new software is that while using a previous program one builds up a set of expectations or assumptions about how things will work (Einstellung, or mental set). In other words, previous experience acts as an obstacle to learning how to use the new program. Give it a bit more time, and you might find you can get over the hump.

Each to their own, of course, but Bookends has served me very well for 10-15 years, if not longer.

Thanks, MBBNTU and NONTROPPO! I appreciate it.

I definitely see the benefit of the temporary citation - especially since the project WILL run into the hundreds of footnotes/sources. So it looks like Bookends is the way to go, here. I just need to figure out how to better import online sources.

MBBNTU, I was feeling restricted in Bookends in terms of how it searches. When I search JSTOR directly for a topic, I get hundreds of appropriate results, none of which showed up when I searched the same topic through the Bookends. So I guess I’ll head over to the Bookends forums to think about this.

I’d love to hear from other academics about their research/writing workflow using Scrivener and reference management software. What does your workflow look like?

What do you all think of this workaround?


I don’t like it. The temporary citation is too long and complicated, which makes it possible that errors could be introduced. I can easily remember some citations that I insert repeatedly, to I can easily type {Smith, 2000 #378} or something like that, without having to break my concentration by switching to the other program. For that reason I would prefer the shorter temporary citations used by Bookends. Of course, one can also use a text expander or a saved clipboard for quickly inserting much-used items.

Edit: if you use the Bookends Browser you can go to the JSTOR web page as if you were using Safari. That will give you the same search tools and results. Exporting the citations and then importing them into Bookends takes an extra couple of steps, but at least you find the same items.

I’ve posted the JSTOR problems to the Bookends forums here: sonnysoftware.com/phpBB3/vi … f=2&t=4763

My workflow uses Bookends to find and store my references. I use DOIs and Pubmed IDs almost exclusively, you can “QUICK ADD” a DOI or PMID and Bookends fill in the rest, the fastest way to add refs for my field (neuroscience/biology). I tend to use my own browser to search, highlight the DOI/PMID — then use an Alfred workflow to copy the text and move it into bookends automagically using applescript. I also have a PDF Watch folder set up so I can add PDFs to my Watch folder and Bookends automatically triggers and adds the PDF, autocompletes the metadata and moves it into my PDF archive correctly named (no user intervention needed, but it does need to find a valid DOI).

When writing, I use an Alfred workflow to search the database in a floating window (like Papers magic citations, Bookends also can do this natively in a recent update), then easily paste using a BibTeX like key into Scrivener. All my writing using the “Hybrid” system (§21.4 user manual), which automates complex document output (equations, figures, TOCs etc).

For the bibliography generation, I use Pandoc-citeproc which automatically creates a bibliography for me use CSL styles in any output (DOCX, LaTeX, TXT, HTML) completely automatically, no need to scan manually after a Scrivener compile.

My workflow is (humbly IMO :stuck_out_tongue: ) the fastest and most streamlined, but at least optimising the Pandoc final formatting requires a certain level of technical knowledge.

My Alfred workflow that collects 11 different tools is here: github.com/iandol/bookends-tools

Jon has already fixed the JSTOR parsing in Bookends browser (you can directly import references now), and the problem with direct JSTOR searching is an issue in the JSTOR API, not bookends. This is a major reason why Bookends is such a great reference manager, a direct reply with a working update direct from the developer in less than 8 hours!!!

The “temporary citation” approach seemed quite enticing, but I realized that my version of temporary citations is often just a footnote for myself that reads “Cite that book by so-and-so on that thing” for a while, until I go back and add a formal citation.

To link Scrivener and Zotero, I use Alfred (basically a keyboard wizard type utility for Mac) and a free workflow (ZotHero) that bridges the gap. It saves two steps, essentially: I press option-space, type ‘zot’ followed by author or title or keyword or anything that will find the record in my Zotero database, then option-enter will copy the full, formatted citation (in the output style Zotero has selected) and then just paste it into Scrivener. I value not having to lose focus from Scrivener while working.

Hi. I’m an academic and use Zotero with Word currently.

My friend and colleague told me about Scrivener and it’s really going to be a game changer for me. I’ve done the tutorial and I’m ready to get started. I’m trying to get my head around the following:

  1. how do import word docs that have been created with Zotero (and maybe some older ones I created with Endnote…but baby steps). And 2) how I will go on using Zotero as I go forward.

This thread seems to given me some answers about 2). What Lfree describes is close to how I use Zotero with Word now. I always generate the final bibliography in a separate word doc from a Zotero folder that I create for each project. For the citations themselves, I first create a footnote with Word and then add in the citation with the Zotero toolbar. This is because I need to add a ton of text in my footnotes. I use the feature through which you can modify the citation with prefix and suffix text, which would be a shame to lose. I also use the function to enable me to create a string of more than one citation in the footnotes.

I have a few questions, which may sound amazingly idiotic (because they probably are) but…

  1. Is any of what I currently do as described above going to be possible? If not, they should be something that I could then do once a final chapter or article has be exported into Word, yes? Although this is a bit annoying.

  2. I need to retain the functionality of having the references update when I make changes in Zotero. I also need to be able to change the style of bibliographic citation. Is that still on the table when using Lfree’s method? Lfree are you copying a final formatted text version of the citation, or the electronic version that can be updated?

  3. Is what Lutefiasco does with ZotHero going to benefit me more? Will it retain any of the current functions I rely on?


I’m an academic (retired) and I use Bookends and Scrivener.

You should probably read the Zotero documentation here: https://www.zotero.org/support/rtf_scan

You will no doubt have to adapt your workflow in some way. But I doubt there is any problem that cannot be solved in some way with the help of people here. This is one of the most knowledgeable and helpful forums on the net.

From what I can gather from reading these forums for many years, most of us use the technique of inserting temporary citations into the text in the form of {Smith, 2006 #1234}. Multiple citations are just {Smith, 2006 #1234; Jones, 1998 #3456}. We then compile the completed text to rtf, and scan with our bibliographic tool of choice. Bookends will certainly use prefixes and suffixes of the kind you mention. Page numbers as suffixes, for example, are preceded by @. I imagine Zotero has some similar method, but you would need to read the documentation.

I know I haven’t answered all your questions one by one, but I am not a Zotero user – I can only say that the sort of work you do is done by many of us using Scrivener, and if Zotero does not work well with Scrivener, I would ditch Zotero and find another bibliographic database!! Scrivener is far too good to pass over.

Best of luck with it!

I am able to use Zotero with Scrivener, on the Windows platform, following the instructions in the URL provided by @MBBNTU

The steps are:
(1) In Scrivener, insert a citation in the body of a text document, using the one of the supplied formats, e.g. {Anderson, 2016} . Note that you should insert the citation in the body of the document, and not in a Scrivener-style footnote.
(2) In Scrivener, insert {Bibliography} in the body of a text document, in the spot where you would like the Bibliography to appear (assuming you want the references at the end)
(3) In Scrivener, compile the document, using RTF as the output format
(4) In Zotero, go to Tools > RTF Scan. Zotero will prompt you to select input and output files. Select the RTF file that you created in the previous step. You can also select an output file, or you can accept the default file created by Zotero. Click Next.
(5) Zotero will display a table and ask you to confirm any ambiguous references. Ensure that every Citation listed in the table has a corresponding Item Name. i.e. if the “Item Name” field is blank, you must select a Citation. Once you have done this, click Next.
(6) Zotero will prompt you to select a citation style, e.g. MLA or APA. Select a style and click Next.
(7) Zotero will confirm that your document has been scanned. Open the document and confirm that the formatting is correct.

That’s it!

I’m glad you got it to work. I’m a little surprised that you can’t put temporary citations in footnotes. I can certainly do that with Bookends on Mac.

Hi and thanks to those of you who have posted on this thread today.

I’ve been trying to work out how to use a reference manager simply with Scrivener for a while. I’ve given up trying to get Scrivener to talk to Qiqqa and a few months ago I moved to Zotero in the hope that it would somehow play nicely with Scrivener.

I did find some rather complicated videos and instructions which sounded a bit to techy for my liking - but I have yet to try those suggestions. I was, however, pleased to see the post by B00KGRRL earlier today as I’ve been wondering how to tackle this problem for a few weeks (first paper deadline looming!) I tested the instructions given, and whilst I had to manually cut and paste the references, it did work quite well and is a simple workflow.

I’m sure it can be better, and if there is a way to link Zotero directly to Scrivener to select and insert the references automatically that would certainly help.

However, bare in mind that Scrivener is an authoring tool not aimed at the academic market (and there has been much discussion on this issue) I think this is an acceptable work around to get started as the workflow is reasonably straight forward. I now feel I can at least develop my document in Scrivener and capture the appropriate references with some degree of confidence before I have to haul the manuscript over to Word to finish it off.

If I can develop 80-90% of the document in Scrivener then I can put up with doing some final edits and polishing in Word.

Here’s a quick video showing the exact steps I took:
useloom.com/share/6fefc627a … 568ee39264

If anybody has any suggestions on how I can improve this process and do more (all???) in Scrivener I’d welcome any suggestions and feedback.

Kind regards


Have a look at the documentation for Quick Copy on the Zotero site, and their shortcuts:



It will save you a bit of time. You don’t need to copy the name specifically, if I’ve understood things correctly – just select the item in the list. Their documentation could be a bit better, though.