preferred reference manager for Scrivener

I know there’s been a ton of discussion of reference management systems and Scrivener on these boards. But I’m new to Scrivener, working on a scholarly book project, and – desperate not to waste time or money on this – hoping to stand on the wise and tall shoulders of those who came before me. I’ve never used a reference management system before, and I’d rather not plunk down a pile of cash for Endnote. Given this, can someone tell me …

(a) Has a consensus emerged as to which alternative system (Zotero, Sente, Bookmarks, etc) works best with Scrivener?

(b) Are there step-by-step instructions somewhere for how to integrate whichever is the preferred Endnote-alternative with Scrivener? Seems like a lot of anecdotal, trial-by-error guidance out there, but nothing authoritative from what I’ve seen.

Your help and recommendations greatly appreciated!


Generally speaking, when using a bibliography manager with Scrivener, you use the manager to create a placeholder code. Paste that code into the Scrivener document, and then when you’re done use the manager to scan the final document and replace placeholder codes with citations. From Scrivener’s point of view, any tool that can accommodate that approach will work equally well.

I’m sure others will chime in with specific recommendations. I’ll just suggest that you review the documentation and make sure that the software you choose offers RTF post-processing as an option, rather than insisting that you do everything in Word.


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Indeed, most reference manager works just fine with Scrivener, the greater problems are what comes after, and that depends on what format you’ll compile to (and formatting requirements of your subject area)…

As an aside, although I get Endnote free from my University, I finally upgraded to Bookends as both it and Scrivener are in a September 2014 bundle offer from Macupdate (I have a second Scrivener licence now to give to a friend):

Bookends was my RM of choice anyway after having trialled Mendelay, Zotero, Endnote and Sente (but as all of my colleagues use Endnote I’ve been locked to that for too many years!).

Thanks for these really helpful replies!

Maybe it’s just me (remember: I’m new to refernce managers in general, not simply in conjunction with Scrivener), but I wonder whether all of these programs are really comparable when it comes to the writing process itself though. The process of inserting a citation (not to mention inserting any nonstandard version of one) seems so cumbersome and awkward looking in the ones I’ve looked at that, despite the fact I’m beginning a 100-120,000 word project, I’m tempted just to wing it like I’ve always done when working in Word. Is any one of these programs particularly user-friendly? I’m going to have a lot of citations, and the bibliography is going to be quite large, and I really don’t want to have to interrupt the writing process by 3-5 minutes for each and every responsible (i.e. not merely place-holding, “I’ll come back to it later”) citation insertion/refernce addition. Ya know?

At least for me, “insert a placeholder and come back to it later” is almost always the best approach while actually writing. Checking citations comes later in the process. Where citation managers really shine is in their ability to simplify replacement of the placeholder with a complete, correctly formatted citation.


Since with Bookends at least, and I imagine Sente and some of the others, when you set up Bookends as your reference manager in the Scrivener Preferences, and you set up Scrivener as your wordprocessor in the Bookends Preferences, from there on it’s like falling off a log … When you want to insert a temporary reference, you press Cmd-Y in Scrivener, Bookends opens and you choose the book, article, whatever in the reference list, press Cmd-Y again and you are taken back to Scrivener and the temporary citation is pasted in where the cursor is (It usually takes the form of {Author, Date, and a Bookends specific reference number} and you can also insert page number at this point if you wish).

When you finally compile your text, if your wordprocessor is Nisus Writer Pro, Mellel or perhaps Word, you can scan the document from within the Wordprocessor and it will substitute the full citation in the form that you have told Bookends you want, and simultaneously create the bibliography for you, again in the appropriate form.

I imagine the same is basically true of Sente, Papers, Endnote, Zotero, and of other wordprocessors … though you may not be able to do in-wordprocessor scanning with some or any of them.

Mr X

A couple of observations and some advice.
First, don’t diss’ the “I’ll come back to it later”. When you’re in the groove writing, a well placed, “<<insert reference to Jones and Smith (I think, maybe it was Georges et al. - check the big black book in the office) here>>” can keep you moving while simultaneously giving you something productive to do on those days when coherent sentences seem mythical.
Second, if you know the reference, and it’s in in your reference manager, it only takes a few seconds to insert.
Now for the advice: do not write a thesis/dissertation without using a reference manager. Do not “wing it” unless you go to a mythical “Happy University” where there are no academic styles and no one really cares whether the commas are in the correct place or if every citation is referenced and every reference is cited, then you will need a reference manager. Tracking, managing and accurately referencing hundreds, if not thousands, of citations will eat weeks (if not months) of your time. Don’t do that to yourself. Have some pity on your time poor and stressed future self and invest in a decent reference manager and learn how to use it now.

Whether it’s Bookends, Papers, EndNote, or something else doesn’t really matter. EndNote is powerful. Papers is user friendly. I’ve heard good things about Bookends. Some people use Sente, some even use (and apparently like) Zotero. Set aside a day to try few and compare them. Make sure that any you like will compile the citation style you need to use, and then choose one, buy it and forget the rest.

I made a lot of mistakes when writing my thesis, but the one thing I did early that saved my sanity at the end was invest in a decent reference manager.

I’ve been using Jabref for a while but because of problems integrating it with Scrivener especially the necessity for me to use tools outside of Scrivener to get references included I’ve gone back to BibDesk where I can drag-and-drop citation keys into documents and references into the document that serves as the bibliography. BibDesk’s template mode means I can control the format of the dropped reference and I’m fiddling with an examplar at the moment.

Although my primary reason for reverting to BibDesk is because of its keywords feature as that helps when comparing and contrasting references for literature reviews and journal papers.

An important question when you choose RM is whether you want it to handle only the references or also all the accompanying pdf’s.
Papers do it all, and do it well, and there is a tutorial in Papers how to do that.

BibDesk does it too. (And appears to do it by detault.)

As with other software it is very much a question of personal taste. I have tested several different RMs, but were never satisfied, until I tested Papers. It is not perfect, it has its flaws, but it works for me.
I do all my literature search from within Papers nowadays (primarily Web of Science), and I include the citekeys in Scrivener and then fix the references and reference list after the manuscript has been exported to Word for the final layout according to the journal’s preferences.

I think Sotera, Bookends, etc, can be used in a similar way, but I prefer Papers.

I use Bookends for the job and it works with no hitches at all.

I have used Papers - but dumped it having been stung too many times when they have messed up updates. Sente is not very good at Cite As You Write and Endnote is, well, Endnote.

One thing about Bookends is the Support is unparalleled. I’ve had responses to queries within minutes, and never more than a couple of hours.

Do any of you reference manager evangelists also use DevonThink, and can you comment on how the two complement each other?

I’ve got my personal PDF management all sorted, thanks, so don’t need or want that aspect of a reference manager. A citation manager might come in handy, but not if it means I need to enter everything twice.


Yes. :slight_smile:

I did import all my academic PDFs into Papers, but then indexed my Papers folder in DT so that I could continue to search them there. A very handy function in DT.

Of course, you don’t need to import your PDFs into your reference manager, but it does help. Most of the reference managers can use the PDF (or the source website) to auto-populate the citation data which can save an enormous amount of time. If you don’t do this, you will need to either manually enter the data or, if you have the source websites handy, visit the site of each one and download the citation data (typically as an RIS or EndNote file; assuming they are academic sources of course). You could also use Google Scholar to download the citation files, but it is not always accurate.

An in-between action, if you already have an established research library, is to only import references that you cite into your reference manager. Without going into detail, I did this with EndNote when writing my thesis. Saves time, while still making referencing easier.

Endnote has a Student version which the OP would be eligible for and it is worth checking to see if you University has a contract with Thomson that gives you access to it cheaper. (I guess many Uni’s are making the online version of Endnote available to their students now. Can’t speak to how well that works.)


P.S. I have been an Endnote user since version 1.0.

Please excuse this question if it sounds a little moronic, but am I right in understanding that Scrivener doesn’t actually do the referencing and bibliography even when you use a manager like Zotero or Endnote?
I’m about to start postgraduate studies and as someone rightly pointed out, the bibliography has to be done precisely as the institution asks or else you get penalised. When I was doing my BA I used OneNote to do all of my research and rough drafting and I would add placeholder inline citations (Smith, 2013, pp. 79-85) and then use Word’s inbuilt referencing system once I copied and pasted into the document. This system was a little cumbersome -especially having to manually enter the bibliographic details into the Word referencing system- but it worked adequately.
So, I’m new to the whole RM thing and it sounds as though I need something if I’m going to be serious about further studies and even writing in the future. I’ve been looking at Endnote -which I can get as a student discount- and Zotero. I know that there will be people out there who love/hate both or either of these, so I’m not so much after a review as I am an indication of the benefit of using an RM compared to the somewhat flawed system I used while doing my BA. Like I said, the question may sound moronic, but having never used anything other than Word’s inbuilt RM I’m a little confused. :blush:

I can speak to the question, though based only on my experience with Endnote.

A RM stores bibliographic information as data, rather than as presentational text. This means your reference database is neutral as to bibliographic formatting standards. This in itself is a virtue of RMs.

When it comes time to put some in-line citation into your text or footnote thereof, you can place a likewise bibliographic-formatting-neutral temporary citation,* e.g.,

{Smith, 2013 #3052 pp. 79-85}

Later, when you want to produce a finished version of your paper using a particular citation style, you have your RM application process your paper to make a copy in which temporary cites are replaced with formatted ones in your choice of style and a bibliography section (if the chosen style requires it) is added at the end of your paper likewise. In the case of Endnote, I do this by Compiling my material from Scrivener into an rtf format file – which Endnote can process directly. I then massage the finished result in Word.

Result: my bibliographic information is stored as data and in a universal database not attached to any particular project, my master copy of my work uses plain-text bibliographic-style-netural proto-citations, and I can produce finished versions of the paper in any bibliographic style required. All these are virtues of the RM approach.


P.S. Word has a built-in reference management system??

  • Some RMs (including Endnote) have some very advanced WYSIWYG features that can put specially formatted code in, e.g., a Word document. But these features are very susceptible to future breakage, so taking the long view suggests that you should use plain-text temporary citations in your documents.

I use BibDesk (a Mac application to create and maintain bibtex data files). It has a drag-and-drop feature that can format the selected references for a bibliography without having to mess with a word processor or other reference manager. There is, of course, a feature to insert the citation text too.

The format of the dragged-and-dropped references is user definable with an XML-based specification format. I created myself versions for the journals I submit papers to. I no longer need to post-process projects and definitely no need to open the Compiled project in a word processor any more. (Though for aesthetic typography I will continue to Compile to LaTex and produce the best possible typesetting for the few documents that need it.)

Personally I think the lack of in-built reference management is a major omission for Scrivener. I hope the hole gets filled in with a later version. BibDesk is a good work-around but I’d prefer to have any other application in my workflow.

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Having to manually add in every reference into word, and not have this information easily exportable or modifiable, or manageable sound a nightmare. A RM has lots of functions to easily import references with all the data and URL/DOI links intact, you can manage them with tagging, notestreams (autoimported from the PDF annotations if you use Bookends or Sente for example) and smart groups so you can find those refs and generate stronger discussions.

A RM is more for my sanity in keeping track of hundreds to thousands of articles than it is to minimise my work formatting a manuscript (which it also does much better than ding this manually)… 8)

It seems to me that much of the potential usefulness of a reference manager is lost if it’s tied to a particular word processor or, worse, a particular word processing document.