Devonthink vs Bookends

I’m missing why people use Biblo mgrs like Bookends if they are already using DT for a filing and storage vehicle for massive numbers of PDF files?

What am I missing?

I use a reference manager (Zotero in my case) for cite while you write (CWYW) features and managing the citation in individual manuscripts. I have all my PDF’s indexed in DEVONthink for research and reading the articles.

Would you mind expanding on your workflow slightly? I’m really interested in the interplay between the two and the benefits and whether I could adopt this into my own work.



It starts with me searching for journal articles using Google Scholar or my DEVONagent search sets. When I find an article I want, I clip it to Zotero using that browser plug-in. Now I have the PDF and all the metadata needed to cite the article in a manuscript:

In the background, two things happen:

  1. Hazel recognizes that a new PDF was added to Zotero and runs Zowie on it to add the Zotero link to the PDF.
  2. My Zotero database is indexed in DEVONthink, so the PDF shows up over there in my smart group to read.

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I then read and annotate the article in DEVONthink. Those markups show up for me whether I am in DT or Zotero, since it’s the same file. I can create collections of references in Zotero, or use DT’s AI and search features to find connections between articles.

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When I am ready to write, I used LibreOffice with Zotero’s citation tools installed (I can do the same in Word, but prefer LO):

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I can write something, quickly add the citation which is automatically formatted and added to the works cited page:

As I edit and rewrite, Zotero manages the citations, making sure that everything is formatted correctly and if I add or remove an in-text citation the works cited is automatically updated. And if I need to submit to a journal that requires a different style, Modern Humanities Research Association, for example, it’s three clicks:

I get to use each app for what it’s best at, but all using the same PDF.


Oh, and I can be at work on a Windows machine, find an article I need, clip it to Zotero there and it syncs to my Mac at home and all this just happens…


Bookends (BE) is designed from the ground up to manage PDFs as citation resources. Devonthink (DT) is designed to manage documents as resources. The two overlap in that they both have tools to manage documents as resources. But BE has tools that DT does not have (and will never have reading between the lines for discussions that can be found in this forum), and the lack of those tools is a hinderance at some point in a productive workflow with citation resources.

Specific to BE, some of what you do not find in DT include the following:

  • Direct BibTeX support (recently enhanced to rival what is found in Zotero)
  • Directed library searches (PubMed, GoogleScholar, …) on journals only

The annotation tools in BE iPadOS are well-designed.

Overall, my experience managing my PDF bibliography databases cause far less friction when I work in BE rather than in DT.

FWIW, I also experience less friction using BE versus Zotero. This is perhaps more a matter of personal taste in design and workflow rather than it is due to limitations in Zotero (which, unlike DT, has plug-in specific components to help manage citation resources).



I would tend to agree as to the idea that BE serves complementary functions to DT. Both programs state so, and there’s a reason for this. I confess I am making suboptimal use of both (and either) and I am writing this as a way of helping myself.

Also, granted that the answer obviously depends on the field (and profession). For example, I am an academic lawyer whose work includes legal history. I have been unable to insert Bookend citations into my papers but, apart from the collection of documents, Bookends allows me to prepare a bibliography (which I can change depending on the format). This came in really handy on my last book – I literally decided it was worth the effort to prepare a “bibliography” database even in the last minute. Bookends has a notes field and annotation functions, but I have never really used them. I could see for some people a distinction made between reference notes kept in Bookends and smart notes kept in DevonThink (I am now reading the Sönke Ahrens book on Taking, along with Kourosh Dini’s book on DevonThink), but I think I will be using DevonThink for both.

Another separate function is that I can distinguish between the pdfs of journal articles, books etc., which I include in Bookends, and all material (e.g. draft papers, working documents) which I can include in my DevonThink database. I can use DevonThink to handle a mass amount of case law but I would not think of using BE, though maybe it could serve a “list of authorities” function.

One of my 2022 projects is to better organise my work/material into DT databases and integrate with my BE database. My real dilemma is where to store the PDFs: right now, I have my Bookends PDFs in an iCloud folder. I would like to include them to DevonThink with its superior search, etc functions but I am concerned because I use more than one Mac, so I may still migrate them or duplicate?


Thanks for sharing your setup and process, including some illustrative screen captures! I’m sure it will be of use and interest to many people. :slight_smile:

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I will preface my comment here by saying I don’t actually use Bookends or similar right now, but that is solely because I’m not doing academic writing at present (the last couple of years I’ve proofed and edited instead). However, if you are in academic writing (whether that’s papers, reports or books), you NEED a citation manager.

Do not be writing your citations manually. You will cry, and if you’re passing your report to someone else to proof (me!) and then Design I will hate you a little bit if I change something and then have to spend a few hours correcting all your citations before it goes to Design.

I love the example cited above in detail, and think that the process is the same for other sciences (I’m in the earth sciences). I personally only want/need a citation manager to be holding the citation data for my library, I don’t need any file manager functions. I was happy with my own files for actual reading and note-taking prior to adopting DT, and now I’m in DT I’m happy with my note-taking and pdfs living there. If I go back to report writing, I will have a similar set-up to that described above with reading and research taking place in DT and an automated citation manager keeping all the citation info for me.

I use Paperpile as my reference manager. All PDFs are stored in Google Drive. I índexed my Google Drive folder in DT to do everything I want with my library. I have the best of both apps. You can use this strategy with any reference manager.

DEVONthink and Bookends do work brilliantly together and really are very different tools. One other reason why Bookends might be a good addition to DEVONthink is that, if your academic PDF library is very large (as mine is, from doing many long literature reviews over the years), there can be performance issues having the whole thing in DEVONthink:

My experience is different. I have 10,000 PDFs indexed in DT from Google Drive. Everything works very well.