I'd like advice on workflow for DT + Reference/PDF Manager

I come from a Windows setup with Mendeley to organize my thousands of PDFs (Name_Year_Title). I switched to Mac partly for DT and I stopped using Mendeley because of several issues with it. Since switching to Mac, I’ve been able to get by without a reference manager and just using manual references that I then fix through my Windows setup, but this is an awkward solution since it created a gap between my Windows reference manager and the growing PDF library on my Mac. I had issues with the Reference Managers I looked at. Maybe I just didn’t have the patience to find workarounds. Does anyone know what Reference Manager I should use, given the following needs:

  • Integrated PDF Library + Reference Manager
  • Using Reference Manager to import PDFs and rename them according to the meta-data, using a format I can specify)
  • Cite as you write (I want a shortcut to trigger a search box inside of Word—unless I’m doing something wrong, Bookends seems to force us to switch windows)


  • Platform independent (problem with Bookends)
  • No odd folder hierarchy is imposed on the PDFs (problem with Zotero)

I might have to compromise with the last two concerns.


All told, the best macOS integration is found in Bookends. It will satisfy your first two points well. I don’t use cite as you write, so I cannot comment on your concern. If the current behavior for this in Bookends is a deal-breaker, perhaps you should ask on the Bookends support forum for insights on whether and how this problem could be addressed.

With cross-platform as a priority, common choices for a PDF library + bibliography management app are

  • Mendeley
  • ReadCube Papers
  • EndNote
  • Zotero

You’ve eliminated Mendeley and Zotero. If you won’t pay as high for EndNote, you might consider ReadCube Papers. You will not be able to rename PDFs with as much flexibility as Mendeley (or Bookends). And again, I cannot speak to the ability for cite as you write within ReadCube Papers.

Finally, you do not say why the app must be platform independent. Are you going to work on both a macOS and Windows system? Or are you going to work on a macOS system and need to share with folks on Windows system?

FWIW, I’ve also given up on Mendeley for my own bibliography management. My transition out involved exporting all references and PDFs, then importing into Bookends. I share with colleagues on Windows using the recently added markdown export option, e.g. to create a shared report for Obsidian.



Use Paperpile. Index your Paperpile library in DT and you will have the best of two worlds.

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@SeferTapuach, take a look at this video about Bookends and Hookmark: Learn from your PDFs and write better papers faster by using Bookends with Hookmark - YouTube and then this video about DT3 and Hookmark.


I suggest Bookends too. Besides from the fact it is Apple only in my opinion it’s the best solution.

One way is hitting CTRL for three times when Bookends is running. Then a floating citation search field pops up. Not exactly in Word but your document is still visible.

When you link an app as Bookend’s word processor you can switch between the two apps by hitting CMD-y. True, this does mean switching between apps but using the left hand to switch back and forth and the right hand for picking the reference is really comfortable at least for my muscle memory.

Sadly, Word uses CMD-y already and is quite intractable when trying to change it in macOS preferences. This might be because the preferences need the exact menu item name to link a shortcut to and in Word CMD-y is linked to the varying Repeat: [last action]. Or maybe just because it’s Word.

So another suggestion of mine is to use the amazing Scrivener to write (and cite) in. You can still use Word for the final formatting including Bookends replacing its temporary citations and generating the bibliography.

One last suggestion: Have a look at the clipboard manager Paste (or any other clipboard managers, if you prefer). I have set one of its pinboards to Bookends citations only so I have a number of recently in use references right at hand—even on mobile devices.


Bookends tends to be more robust than Zotero on many areas. Zotero needs the support of ad ons to catch up with many of the functionlities of BE does natively. And, the ad ons are sometimes unreliable. The developers could dump them in a version; and you would be hanging there hoping sb else will update the ad on (Zotfile for Zotero 7, for example).
There are many other advantages of Bookends over Zotero: some mentioned here recently: Tinderbox Meetup Video- Saturday, July 22, 2023: A Review of Bookends--Citation and Reference Management--with Jonathan Ashwell - #10 by Desalegn - Training Videos - Tinderbox Forum

But, if you have a lot of reference management to do, my advice is to use both Zotero and Bookends.

  • both have strengths and weakneses. Zotero is best at collecting information from the internet. Bookends is best for cleaning up, organzing, renaming and managing references locally.
  • they can be integrated using bibtex as a middle ground