How to use bibliography and references?

I would like to write my thesis in Scrivener but I was not able to figure out few things related to bibliography and references.

How to build a bibliography section that would be based on all references metadata across the project or folder. If the only way of compiling the references is inside each page, this would make this feature almost useless.

I was able to successfully insert references for each document but I would like to be able to insert hyperlinks inside the text to the bibliography entries.

Probably some of you will suggest me to use the footnote feature but there is a problem with this: if I use the footnote feature for bibliography I will not be able to use it for normal footnotes – you cannot combine bibliography references with normal footnotes.

Also, I do not want to add another step after the project compile, or to use ten other applications to solve the book management issue.

This may be related to: [url]] and

Any ideas?


It is best to use a dedicated program for this, such as Bookends, Sente or Endnote. Although you say you don’t want to use another program or to add a step after compile, this is really the best way of doing it, and is what most academic users do, I believe. These programs have been developed especially for such tasks over many years, after all. We do really need to put a video together on using these programs with Scrivener, which is high on our list.

I’ll let other users fill you in on how they do things though, as I’m no expert at such bibliography managers - I’ve always done such things by hand.

All the best,

Hello, I searched for this and I too am looking for a good way to draft my dissertation. I just tested Scrivener and generally it looks really nice.

But proper Bibliography generation based on auto citations is an absolut must.

While I dont mind some not so nice looking tech fixes, managing the bibliographies in e.g. Zotero or Endnote and writing all the curely { } doesnt really fit it. Because I want to have my notes, synopsis etc. on literature I read and my text in one place. Scrivener could do it, with Texts in the Research Section. Zotero can do it too, with its biblometric tree. But I want it all in one place!

Thus unless I can figure out a proper solution, I must refrain from Scrivener and all its coolness and use Zotero/OpenOffice classic.

I don’t really understand your objection if you are already using two programs for this - Scrivener and OpenOffice. But if that works best for you, fair enough - I wish you the best with the rest of your dissertation.

I am not going to try to build a whole separate application - a bibliography manager - on top of Scrivener when there are already great programs out there that work fantastically with Scrivener, just as I have no intention of turning Scrivener into a layout application or database - Scrivener is a first drafting tool. After reading this thread last night I did a quick test with Endnote and Bookends and it was really, really easy to manage citations and generate a bibliography at the end of the process. We have many, many academic users who use these programs together without any problem. We’ll put together a tutorial as soon as we get chance.

Bookends interacts nicely with Scrivener (a keyboard shortcut will call it and will insert a citation, so not that different from using Open+Zotero); Zotero will also still work via rtf scan. It doesn’t work perfectly (since it lacks some of the functionality of other programs that will scan an rtf file), but it’s free and will do the job with some clean up required (my guess is that you will need to do that with any citation manager in the end) and of course you can get information into it with great ease. Those are the possibilities I have worked with and I think either way you can’t really go wrong. If you’re thrifty the choice is easy (Zotero is free); if not, Bookends has a trial scheme–give both a shot and see which one works better for you. Also, Sente and Endnote have trials as well, but maybe others can talk about them: Sente has some nice features but isn’t as good for the humanities as Bookends or Zotero; Endnote, well, I was traumatized by Endnote 7 (?) early in gradschool and never really forgave it, plus they tried to sue Zotero.

In any case, if you need stronger integration than what might be achieved between Scrivener and a citation manager, go buy a PC and a copy of Nota Bene. (

@Sorin, you may also want to check Mellel and Bookends. Its integration with Bookends is excellent and I like them better than Zotero/OOo. But it’ll cost you some money.

I certainly wish Scrivener had a better integration with Bookends or other managers, but for a first draft tool you can definitely do a lot with it and you quickly get used to the curly brackets. And if you use footnotes, they are pretty much out of your way.

Well thank you for the fast answer!

My Objection is that in social sciences and humanities drafting and managing bibliographic sources is one process. For every source I make notes on idea, or write text around it. Normally I use Zotero for that, as it manages all your notes as nodes in a tree, too a large extend like professional qualitative analysis software does. And the normal process is then to write a linear text using that in an office package using zoteros citations addons.

Now when using a drafting tool like Scrivener, I want my notes, synopsises and ideas to be there in Scrivener along with the text drafts and not in Zotero. And yet I do not want to keep dual databases like having a “notes” part in scrivener, and managing the citation from Zotero, in that case I can have my notes directly back to Zotero.

Well I hope it sounds not too strange what I’m saying. Traditionally some people in that field use “card boxes” a lot, physically, a card for every source, a card for every idea, a card for every text note. Scrivener seems to work a lot like cards for drafting, except well if you have cards for sources, you still need another database for the source for the citation.

I do understand your notion to focus on one aspect for your application to be good add. I just keep on searching to find an electronic “card box” solution, that is able to hold all that cards, and at the same time compile papers. Nevertheless If a friend of mine looks for a pure drafting tool, I’ll sure advice scrivener, especially since its now more “accessable” due osx+win.

@howardtheduck thank you for you answer. Actually I’m not really thrifty, as long its not really expensive. (>100,-). However I worked both with Zotero and Endnote (got a version X license) before, and can say, for me Zotero proofed to have better. Especially I like the synchronisation with its online database. Altough there are some nasty little surprises, like having only one global language setting, and if you have multiple documents in different language, be sure to always set it correctly, before handing a paper in. And Thank you, I will give Nota Bene a view, didnt know of it. I’m not fixed to Mac or PC, I got all of them around :slight_smile:

I guess I still don’t understand the problem, sorry - my own background is in the humanities, have studied modern history for my BA and medieval studies (history and literature) for my MA and (never-finished) PhD. Scrivener grew as much out of the way I wrote dissertations as out of my desire to write fiction. Although I used to maintain a bibliography manually, making a quick reference to the text in the footnotes that I would fill out later, bibliography software such as Bookends pretty much takes that manual step away and fits into the process perfectly, in that such software inserts citations (akin to my old notes, “Pearson - Chaucer p81” or whatever) that will later be formatted for you in the scan (the part I would do manually at the end of the process).

I guess I don’t understand why you would keep all of those notes in Zotero rather than Scrivener, but everyone has different workflows and obviously you need to find the best one for you. Good luck!

All the best,

I will add that another free, powerful bibliography manager exists: BibDesk. It needs some initilal setting (creating your templates, maybe adapting them from existing ones), but it is nice.


I just want to keep the notes around the source and the data about the source in one place. Double “databases” manually held in sync is always a bad idea, imho.

I agree with the convenience of having notes integrated to the bibliography software. And Zotero’s implementation of notes is excellent. But for inserting citations, Zotero is really cumbersome imho. Of course, unless you use OOo or Word, but then you get the problems when you deal with a long manuscript, especially if it has tables, illustrations and plenty of footnotes.

Bookends implemented a “note stream” mode a couple of years ago that seems to work in the way you are describing your use of zotero. There is a note field with plain text. Two blank lines separate notes. If you start the note with "@123 " it recognizes that as a page number and will use it in citations. The note stream can be represented as a text blurb or as notecards, very similar to the index cards you mentioned. The workflow gets as easy as:

  1. Scriv: Insert Footnote, Command-Y
  2. Bookends: search piece, tab to the note, use cursor keys to find the note, press command-Y
  3. BE inserts “{Lastname, Short title #98765@123}” in the footnote. After scanning, you get the citation with the page number.

In my opinion, having the curly thing in footnote citations is not an issue at all in most scenarios. (I believe the developer is considering a mechanism to make citations like in Papers 2, which would be even better.) But if curly brackets are the issue, Mellel would give you more of the “live citation” feel, but at the expense of learning a new paradigm in style management and a terrible GUI in my opinion.

I use Scrivener with EndNote and Papers for writing my doctoral thesis and am considering reducing this to just Scrivener and Papers 2. Not really sure what the problem is with using 2 applications (since I currently use 3!) as long as they each do their job competently and work together well.

Scrivener: writing and notes
Papers: storage of research articles
EndNote: bibliography and citation management once I have compiled my document in Word. You can manually enter the curly brackets {} into Scrivener, or just drag and drop the source from EndNote (or Papers or other bibliography manager of choice).

Here’s another vote for better integration between Scrivener and Zotero. I found this promising post: … g-zot.html I tried it, and the process went fine, right down to Zotero asking me if these were the citations I wanted. But when I went to the newly created rtf version that supposedly contained all the notes, nothing showed up, not even the squiggly brackets and citations I typed in. I’m wondering if others have tried this. For academics, footnoting is a weak link in an otherwise wonderful Scrivener, and it sure would be great if there was a reliable work-around short of having to pay for a bibliography program I don’t want or need. I’d be grateful for any suggestions!


You might try posting this on the Zotero forums. They’re pretty good at troubleshooting and legend says they’re in the process of rewriting the rtf scan.

Thanks for this advice. I did post there, but under “feature request,” and someone (probably not a representative of Zotero) told me that the changes would have to come from Scrivener’s end because it’s a smaller operation and Zotero couldn’t be expected to figure out how this would work. I rooted around enough in Zotero to discover that a number of people have had problems with the rtf scan (the export feature that’s supposed to play best with Zotero). I also found some real frustration in the Scrivener forums with footnotes and comments, so hopefully the next version will also take an increasingly-important, free bibliography program into account. I’m going to keep trying, but I might just settle on writing in Scrivener, providing brief in-line cites, then exporting to the dreaded Word or OO (which I’d have to do anyway for publishers) and working with Zotero’s plug-in. I’m skeptical this will work, which might mean having to abandon Scrivener for my academic writing. But just maybe someone has a better idea or could fix this…

Scrivener exports standard RTF with standard RTF footnotes, so I don’t understand the problem. We are a very small team and cannot be experts in everything, so it would make things much easier if a Zotero user could post steps explaining exactly how they use things and exactly where the problems lie.


@Keith. Zotero user here. I’m no coder but don’t think that Scrivener’s rtf export is at fault.
Zotero’s RTF-scan feature simply scans an rtf document for textstrings wrapped in curly brackets {Miller, 1998, 271} and morphs these into proper citations (according to the style chosen in Zotero) and then adds a proper bibliography on the basis of these entries at the end of the text. The endresult has no live connection to Zotero’s database. The documentation for users to this procedure can be found here:

Overall, this does work – I’ve been using it for a while – altough its not perfect and needs copy-pasting for citations and some manual touches here and there. I’ve described the procedure in more detail in another thread some time ago:
There are signs that Zotero’s RTF-Scan feature will be improved upon in the near future:

An alltogether different question would be full interoperability between Zotero and Scrivener with a Plug-in hooking Scrivener into the Zotero database – along the lines the Zotero folks have done for Word and Neo-/Open-LibreOffice. It’s highly unlikely that Zotero’s devs (not many) can be convinced to do this – for obvious reasons. (See eg. bdarcus’ post here):

I would be great if the Scrivener team came up with such a plugin (Zotero is big, opensource, on all platforms, particularly with Scrivener’s Win version coming up and the loads of footnote-happy academic users coming to Scrivener’s goodness, burning to cite from their Zotero libraries…) but it’s probably a good deal of work. (Apparently the Papers2 people have something working along the same lines). While you’d be making quite a few folks happy (very happy) with such a plugin, I’d understand if you have other priorities.

@pommette: The specs for the RTF-Scan need being adhered to quite strictly otherwise the scan doesn’t work. It’s best do define a particular export style for citations in Zotero (Preferences>Export) that produces the necessery curly-bracket-version which can then be copied from Zotero to the Scrivener draft. There is such an RTF-Scan-style here in Scrivener’s forum: [url]]

Also check if your final output citation style (not the RTF-scan-style above) is set to what you really need – if you’ve set a footnoted style in Zotero you’ll not see inline text citations in your final rtf-scanned document.

This issue is a very, very old one on the forum, but it’s worth noting that Scrivener began to support creative writing, mainly fiction and film, not writing that requires professional annotation. The developers have generously attended to journalists, scholars, lawyers, and others; and most of them recognize that Scrivener is fundamentally an organizing and drafting tool. Scrivener supports stand-alone reference managers like BibDesk, Bookends, Endnote, and Sente. If reference management is a big part of one’s writing life, those products are really the best way to go.

PS: Zotero now has a stand-alone product:

Thanks for the information. Unfortunately, we’re an even smaller team than the Zotero guys (and while we don’t have hundreds of thousands of users, we do have tens of thousands that we have to support - that’s on the Mac, who knows how many will come to the Windows version? :slight_smile: ). Thus it would be very difficult for us to write a Zotero plugin - if we (or rather, I) were to write a plugin, it would make much more sense to start with Endnote, as that is much more the standard than Zotero, even though I am aware that Zotero is very popular. But really, everyone has a favourite citation manager - there’s Bookends and Sente too - and we just don’t have the resources to write plugins for all of them; I don’t really understand citation managers, to be honest, given that I used to hand-type all of my citations and bibliographies during my years of academia - it’s on my list to get a good grasp of how to use all the main ones, how they work, so that we can at least provide some tutorials in that area.

All the best,