Using Scrivener and EndNote together on Mac OSX

And so, some time ago I bought a Macbook.  And then I found the killer apps that I needed to write my thesis.  Scrivener, hands down, is the best writing tool on PC or Mac.  There is now a PC version, at least in beta, and although it’s not as mature as the Mac OSX version I believe it is getting there.

There’s so much more that I’d like to write about Scrivener and how it is helping with writing the thesis.  However, it’s not as easy as all that – so I did a video instead.  Voila, one video ‘Scrivener and EndNote’:


You can buy Scrivener from, and EndNote from  Scrivener is not very dear at all (say, $A47.19 at the non-educational price).  So you can’t complain.  Endnote is usually available through a university licence – that software cost me zero to run under the UQ licence (so long as it is for research etc etc).

Anyway I highly commend these two applications to you (although apparently is coming up well from behind as well as an alternative to EndNote).  All worth the price of admission.

[PS:  You might be interested in this other post on my blog, where you can download my Scrivener template for academic papers/writing:  Scrivener – draft academic template for academic writing]

[PPS:  Since writing this post, I have written an automatic style formatter in Word (very rough, very basic, and very ugly) that converts fonts of a certain size to a Heading 1, 2, 3 and 4 style in Word – see this post here:  Scrivener to Word Visual Basic Fromatter].

42 thoughts on “Using Scrivener and EndNote together on Mac OSX”

  1. Hi Michael,
    Thank you for sharing this! I am just getting into using Scrivener myself, and am also writing my dissertation. I’ve been using Zotero, not EndNote, but seeing your ease of use makes me consider transferring my citation library over…
    I would love to see your academic paper template. Would you consider sharing your template file?
    Again, thanks, this is helpful! Most of the Ccivener discussions are focused around fiction writing instead of academic work.

  2. Ah, you noticed the template :). Sure, why not, once I’ve ironed the bugs out of it a bit. I also have a longer video on Blip on how I use the lot (Scrivener, Evernote, and Endnote together). That video is here:

    Some people have suggested using Sente on the Mac, which is quite good for getting quotes out but not quite there in terms of the search capability that I can get using Evernote. But it would avoid having to use three pieces of software (well, four, I’ve just found ‘Papers for Mac’ which also is good but again not quite there in terms of search and retrieval).

    I’m not sure about Zotero and how good it is; EndNote is the default and generally accepted citation manager in my field. Keep an eye out on this blog, I’ll post the academic template in the next week or two.

    Thanks for the feedback: Micheal

    • Hi Micheal
      Thanks for the academic transcript this will be great for writing articles – is there any chance in the near future of a template for a thesis as I am just writing mine up…. if not its cool Scriviner is easily to manipulate !!

      • In my experience you are best off grabbing a thesis that your advisor has already mentored on and following that – as the different areas are quite different I think you might go down a Very Bad Rabbithole if you adopted my structure for your work.

        Although I have first-chapters in with my advisor at the moment so I will shortly know what he thinks of it all.

  3. Hi Michael

    I have written my thesis in word, using Endnotes for my citations (footnotes in my case) and I am thinking of using Scrivener for my final editing process. Do you have any idea if I’ll be able to import my documents with the (Endnote heavy) footnotes intact? No worries if you don’t, just thought I’d check.


  4. Hmmm. Have you used cite-while-you-write or have you embedded the codes using the braces?

    If you’ve used cite-while-you-write I think there’s an option to display those in the brackets, in which case you could import the document simply by copy-and-paste. If you’ve used brackets then, yes, it would come straight over I think.

    It would require a fair bit of mucking about to establish the document as a proper Scrivener document I think though – will the final edit process be fairly heavy editing or are you merely looking to reformat it?

    Because for formatting I’d leave it in Word.

    However if you are looking to tighten the thesis, I’d definitely bring it into Scrivener and break it up into its components parts (command-k will “split” the document) as part of the editing process. That will force you to come to grips with the document at a detailed level and produce something that looks good right at the end.

    Thanks: Micheal Axelsen

  5. I think I’ve embedded the codes using the braces. I want to use Scrivener to tighten up the thesis – help me with the transitions, spotting the gaps, fixing the structures etc… but it may just involve too much mucking about. Right now I can’t even work out how to bring my footnote references (the numbers at the end of sentences and quotes) across when I import the files.

    Thanks for such a quick response though!

  6. We’re probably in the same time zone…

    Hmm. I see Scrivener’s supposed to be able to import footnotes from an RTF:

    “Scrivener can now import annotations, footnotes and images from RTF files. Note that this only works for RTF files, and not for DOC files. Thus, if you have a Word document that contains footnotes, endnotes, comments or images and you wish to import it into Scrivener, it is best to save it as an RTF file before importing it. Note that not all images may get imported – Scrivener can only read certain RTF data. Where it cannot read the image data, the image will just be ignored (not imported)”


    I would import as an RTF, and then go through and use command-k to break up into chapters, and then logical components of chapters (sections, sub-sections, specific paragraphs). It is nice that you can flag a particular component of text as a revised draft or finalised etc. I am using that to goal set my current report I am working on.

  7. Hey! I really appreciated your tutorial. Is there any particular reason you didn’t open the compiled RTF document in Word, and then use the Format Bibliography command? I’m using Turabian’s style, meaning the footnotes are pretty unwieldy – almost a full citation, but not quite the same as the bibliographic citation. EndNote doesn’t seem to recognize the temporary citations when they’re in footnotes in the RTF document when I use the Format Paper command, but it does seem to recognize and properly format them once they’re in Word. Just curious whether you experimented with it and I should expect horrible things in my future, or if it’s just a different way to do the same thing. Thanks!

    • Hi Maggie.

      Mainly because I am ignorant of the “Format Bibliography” command, I suspect. I understand this is part of the EndNote CWYW toolbar, and one of the major dramas I am trying to avoid is using CWYW in Word – it has caused crashes as long as I’ve been using a Mac and Endnote – and I think that although the “format bibliography” command is on the CWYW toolbar, I don’t think it actually uses CWYW. I think it is the same thing though as doing the /Tools/Format Paper in EndNote (and won’t create an extra file on you).

      If you don’t use CWYW I don’t see any real problem with using the Format Bibliography command in Word. But I guess you can’t take that to the bank – I think Word has crashed dozens of times on me when I have attempted to use CWYW and I am a bit gunshy. I don’t trust Cite While you Write to get the ‘correct library’ either – had several episodes of problems with traveling libraries so I don’t risk it now… a few people have stories to tell like this. It’s probably an irrational fear by now, but still.

      Thanks: Micheal Axelsen

      • Thanks for your response. I’ve tried my way, because of the length and placement of Turabian-style footnotes (and I didn’t see your response in time), and you’re completely correct, Word goes slowly and sometimes crashes once you bring CWYW into the picture. Oh well, now I know for next time. Luckily it’s only a 30 page paper, rather than a whole dissertation, which I suspect would consistently crash Word if you’re trying to use CWYW. Thanks again.

  8. Hi Michael,
    Could you type out the key combinations for citation copy and paste?
    After I used “command+Y” to open Endnote library through my Scrivener project, and after I found the reference I want to cite, I used “command+c”, and then “command+v” to the text. But only (***, 2009 #2010) showed up, not your {***, 2009 #2010}; when I compiled the documents, neither can I see any citation in the end of the RTF or Doc document. Where did it go? Did I use the wrong keys? what’s the difference between ( ) and { }?
    I watched your video several times but can’t hear clearly and still haven’t figured it out:( Very sad that I spent so much time on computer skill instead of writing my dist which is due soon.
    Could you be more specific? How do I copy and paste an Endnote entry to my text? Which keys to click? Where do the citations go? should I paste the citations to the “Work Cited” file separately in order to generate a “Work Cited” list in the end of my paper/dist??

  9. Hmm. The keystrokes you are talking about should work fine.

    I think it is probably an EndNote configuration thing. You need the braces (“{}s”) rather than brackets (“()s”) to clearly mark up the text that EndNote is to replace. However, EndNote allows you to change these markers to be anything you want. The ones in my video are the default.

    I suggest you check your EndNote preferences for this (command+, and then select Temporary Citations).

    Are the temporary citation delimiters set up as { and }? I think it sounds like they will be brackets rather than braces; I’d strongly suggest braces rather than brackets, as we never use braces in normal writing. Perhaps change this preference to braces – if that’s what it is – and test on a simple RTF document created by Word or Scrivener.

    Be sure when you select /tools/format paper that you select a new file to output to. That is where the citations will go – right at the very end of the paper. You don’t need to paste a work-cited list manually into your paper (you will likely want to move it from the end of your paper to earlier however, once you are happy with the whole thing).

    A final point – when you compile your Scrivener RTF document, check the date and time of that file. Then when you format the paper using EndNote, you should be creating a new file with a later date and time.

    Hope this helps.

    Thanks: Micheal Axelsen

    • Many thanks for your quick reply. I did manage to change the setting from () to {} in Endnote. and I use command+c & command+v to add citations in my Scrivener essay. But still I can’t see any citation showing up in the end of my compiled draft in RTF file. I can only see my notes.

      Could you specify “Be sure when you select /tools/format paper that you select a new file to output to. That is where the citations will go”? Sorry as you can tell I am really not that good at computer/software.

      “/tools/format paper” is in Endnote; when I chose it and a window comes out asking me to “open” a file: but i can’t “open” any file (pdf/doc) which all appear grey. How do I “select a new file to output to”?

  10. Daisy

    Good to hear that the settings worked there.

    EndNote should ask you to “Open” a file (you should select an RTF document for this – the one you exported from Scrivener). When that’s done it should come up with a dialog box that lists off your citations in the document, identifies whether there are any “unmatched citations”, and it then requires you to format your paper.

    When you click ‘format’ it will prompt you with a location (this should be where your original file was saved) – it will be the same file name as your original file with whatever citation style you selected appended (e.g. yourfilename-APA-5th.rtf).

    See if that helps?

    Thanks: Micheal Axelsen

  11. Micheal Thanks a lot! Finally I got to see my citation in the compiled .rtf document.
    But somehow none of my footnotes show up in the “Note” section which supposedly “Any footnotes you created in your paper will get inserted here upon Compile (this purple bubble will be removed automatically”.

    when I compile my conference paper into doc file; i can see the footnotes; but RTF file seems to rip off the notes. Do you happen to have any clue???

  12. Well here we go, day 3 of different-time-zone IS support :).

    When you compile your document there are footnote options (option-cmd-e), Footnotes/Comments. I’ll bet it’s one of the options in there. Are they actually footnotes, or are they comments? I note that for the .docx format, footnotes will become endnotes automatically; this is not the case with RTF documents.

    Try playing with the settings here, and changing the “Compile for DocX” vs “Compile for Rich Text Format” options and seeing how things change?

    You could also play with the RTF Compatibility settings in this dialog box. I note that this area also plays with footnotes a bit.

    Perhaps if it’s a real drama I’d try compiling to DocX, then saving in Word to RTF, then EndNote compiling, then save back to DocX. Which is a bit of rigmarole.

    You could also try searching the Literature and Latte forums for support:

    Hope thishelps.

    Thanks: Micheal Axelsen

  13. I am hoping that it is something to do with the compilation element of the program. Post back and let me know if you can resolve it perhaps?

    Thanks: Micheal Axelsen

  14. Hello Michael, thank you so much for the video. I have just started playing with Scrivener and was a bit bamboozled about how to use Endnote with it. Your video cleared that up for me very quickly.

  15. Yes, I did give Papers 2 a try but I guess I think ‘too blooming PC like’ as it didn’t work for me. I still like my control and precision.

    I think it may have been that Papers didn’t do what Evernote or Devonthink does for me database-wise, and it may not have gotten APA right for me at the time.


  16. @PlEagleTrainer – sorry, I missed your earlier comment.

    Glad the video was helpful. I still do it this way; flirting with going back to Word (reformatting for academic submissions is a non-trivial exercise) but CWYW just kills me.


  17. Hi Michael, many thanks for your video and academic template. I suspect it saved me 1-2 weeks work, in fiddling around myself when I was getting started with scrivener.
    I’ve a question on putting drawings or diagrams within the text editor. I only have a few, but I like to have them embedded in the text if possible. In your video you mentioned using JPEG, having exported the drawing from Powerpoint. I didn’t manage this. I tried File, Import… but JPEG files are greyed out on my finder. I was able to drag & drop the image into the editor, but it was subsequently lost in the compile. Have you any other tips with regard to placing diagrams in the editor / text? Much appreciate you sharing your insights, Sinead.

  18. Sinead

    That’s good. Glad to help. Promise to buy me a coffee sometime when we meet :).

    What I have taken to nowadays is to do the draw in Powerpoint, save it as a Powerpoint (usually, in a subdirectory called _diagrams of the folder where the Scrivener project is at, and using as a filename the Scrivener figure reference (e.g. <$n:figure:research-model>.ppt) and select the drawing and copy-and-paste into Preview, where I save it as a PNG (or a JPG if you prefer) that I insert into the document.

    Remember to scale the image back (I do it to 255 pixels, approximately) so that when you compile it doesn’t leave the image at monster-truck size when you open it up in Word.

    Similarly, I do tables in Word as Scrivener’s table editing is just awful. I create an RTF document in Word, create the table and format it there (including combining cells etc) and then import the RTF document as a new scrivening into Scrivener.

    Hope this helps.

    Thanks: Micheal Axelsen

  19. Michael, I’d be happy to buy you that coffee sometime. Your suggestions are neatly organized, as always. It’s interesting that “inserting” the diagram or picture into scrivener seems to work better than “importing” it. That has moved my editing struggles forward. Thanks again. Sinead

  20. I have come across some other issues (see my post: Particularly tables and working with other co-authors.

    But then I have gone and returned to using Scrivener after the complete unreliability and lack of capacity of Mac Word 2011 was proven to me.

    But tables particularly cause me the most grief with Scrivener, and I am still trying to get those working properly.

    Thanks: Micheal

    • Michael – at the risk of necromancing this article [now more than a year after the last comment – here’s hoping it gets picked up 🙂 ], I just want thank you for demonstrating what I simply was not managing to pick up/visualise from all the topics on this point, over at the Scrivener forum.

      With this being said – the one potential stumbling block that I am still trying to get my head around, is how to work with really looooonnngggg footnotes. By this I mean – writing in law, apart from (for instance – simply listing a case reference), one would often also discuss the permutations of that particular decision/judgment… The way I see it – you would then have all that ‘footnote’ text “in-line”, as it were, with the rest of your ‘main’ text’s words – is that correct? Or is there a way around this? Since it would be potentially disruptive to have it “interfering” with the flow of your main argument, whereas in Word – that all happens at the bottom of the page, as a footnote proper…? Hope I’ve made sense in conveying my question. If you do pick this up, your thoughts would be greatly appreciated!!

      • Micheal (apologies for the earlier typo) – at risk of having a convo with myself – I came back to answer my own question. I based my earlier comment on an old thread over at Scrivener forum – which appears to have been commenting about Scriv 1.0. Version 2’s footnotes feature appears to have sorted the inline problem – and a test compile/export this evening, using Endnote X6, worked a treat. Thanks again!

      • No worries about Necromancy in this regard – this is one of those few posts of mine that gets visited.

        I think you’ve already answered your own question – V2 changes footnotes dramatically, and they now appear as a callout in the margin of the text.

        You can still do an inline footnote.

    • Also by way of update, I went back to Word for my phd after struggling with tables in Scrivener. New Word seems much more stable, but I do miss the Scrivener functionality.

  21. Hi Michael, sorry for commenting on this thread years after you originally posted it, but I recently came across your video tutorial on how to use Scrivener with Endnote. I have done everything as you suggested, however I use Chicago style (i.e. footnotes) instead of APA (in-text). When I open the formatted document in word, both the footnotes and the superscript number citation are missing.
    The bizarre thing is, if I choose a different refencing style – i.e. APA – the citations become visible in the correct format. So the problem seems to be with the referencing style I have selected, namely Chicago. Can you think of anything that would fix this problem?


Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.