Best Citation Manager?

I know there are several threads on this but I thought I’d start an updated one. I have used Papers 3 in the past but since nuking and paving my MBP a month ago, I am slowly adding apps back into my workflow as the needs arise.

I would appreciate your recommendation for the best citation manager to use within the Apple ecosystem. For research and writing I rely primarily on DEONthink, Obsidian, and Ulysses. For the final product I use Pages.

I do not want to pay a subscription for a citation manager.

What is your recommendation and briefly why? I appreciate the guidance–thanks!

I think it depends on your use case? I use Bookends to manage the citations for my Zettelkasten. It has its weaknesses, but it is native and does interconnect well with Devonthink and Hook.
If you are a power user and you need it more for academic use you can look into the direction of Zotero. I used it before on my Windows machine and it is very good.

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Given the apps you listed, I think Bookends makes the most sense. I don’t think it’s the best citation manager in all cases, but maybe it is the best at playing well with Apple ecosystem?

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I’m using Bookends, and have been for about five years. I have about 2500 papers in it.

One concern might be that Bookends has a mobile app, while Zotero doesn’t. There’s something that people use, paper ship or something like that, but it’s not from the same developers.

I pay the $10/year to support the developer. I don’t remember what that gets me, maybe sync with mobile devices and updates.

Zotero works for me - I moved to it because it was cross platform and I could sync the documents folder via Resilio. Been using it now for probably 6 years.

I’m very partial to Zotero. I have two wishlist items: 1. I’d like to have a mobile app; 2. I’d like better integration with Scrivener. Plugins like ZotFile and Zutilo are key to my workflow.

I’m not, strictly, an academic, so my needs may not align with yours. I’m a lawyer, so I cite a lot in my writing.

Also, I use Zotero more broadly as a key component of my information management system. All my books, articles that I have sourced important information, reading notes, etc. all go into Zotero.


@Schmages @beck @JohnAtl, @drezha, and @iPersuade, thanks for the input!

Quick follow-up question. Will either or both Bookends and Zotero import a webpage and its metadata? With Papers 3 it has the ability to import webpages and extract, when available, the information needed to generate the citation. One can also add information before saving the article.

Thanks again, very much appreciated!

Zotero does extract information from Websites, but I’m not sure what it uses to get the information. I say that because I can clip a blog post, and sometimes it will have all the information correct: author; title; date of post; etc. Sometimes I get nothing. [CORRECTION: This does not mean that the extraction is arbitrary and each time you click it you are rolling the dice. What I mean is that some blogs have whatever information Zotero is searching for to pull out the information, others don’t.]

Zotero also does pull in the complete page you are looking at, so you can read it offline, etc.

Beyond the scope of your question, but possibly useful as it relates to extraction of data … It can extract information from PDFs, too, including TOCs if the PDF has them. The PDF has to contain the appropriate metadata, of course. But the TOC function is great because you can click the link and the pdf will open and go directly to the TOC page. You can also extract your annotations that you make on a PDF.

Thanks, that sounds very promising. Have you had any experience with Bookends and if so how would you compare Zotero with it? If not that is fine, I just thought I would ask. Thanks again.

I have no meaningful experience to share. Bookends was recommended to me, and I tried it out briefly. Zotero just clicked more with me for some reason. I do not have any useful (i.e., objective) information to share about Bookends’ workflow, features, pros, or cons that might help you evaluate your options.

@iPersuade Thanks again. I’ve downloaded Zotero and just finished reading some preliminary information and the Starter Guide. It seems like a no brainer to give Zotero a try—its free, open source, and full featured. Assuming it works as advertised, I can’t see how one could ask for much more. :slight_smile: Thanks for the tip and replies! I owe you one.

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The best recommendation can vary depending on your field of interest. Hard sciences versus engineering versus soft sciences versus liberal arts versus medical versus … It can also vary depending on what you mean by citation manager. Are you using it to administer the citations and more so than the documents that belong to those citations? Are you using it to search for similar literature to specific citations? Are you using it to store a huge database locally or to network with others? Are you using it to store a huge database that you also need to access on the go?

Can you expand on these questions a bit?


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Certainly, and I should have included that contextual information.

At this point, my needs are far simpler than they were when I was in my doctoral program. I store all of my research articles and book annotations in DEVONthink natively and/or indexed to Finder. My only use at this point is to input research articles and book bibliographical information in the citations manager so I can cite while I write and create a bibliography for a big book project I’m working on. Otherwise, I only need to grab the citation in APA format when quoting or paraphrasing material for articles and presentations (I insert citations in my Keynote slides so I can share the reference if asked or needed). I’m a stickler for giving proper attribution.

@iPersuade, so far, this is working great! I used the Zotero Brave extension to insert bibliographical information directly from Amazon. It pulled in everything I needed except the ISBN number. It generated the reference below.

Kotter, J. P. (2012). Leading Change, With a New Preface by the Author (1R edition). Harvard Business Review Press.

That took all of three minutes from start to finish. This was far easier and more reliable than Papers 3.

I’ll have to figure out how to generate the bibliography in Word when needed but I’m sure that will be easy.

Thanks again!

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Zotero is open source and has an active development community. But it just doesn’t have the funding to compete with a commercial product.

Bookends has a developer who is very responsive to inquiries and clearly views the software with a passion. So it is “commercial” but in a very. positive sense - and its support of Applescript really helps with 3rd party integration. You can do some integration with Zotero usign the BetterBibText and other plugins, but it is no match for what you can do with Applescript.

Other than Bookends and Zotero, most of the alternatives are commercialized in a negative sense by companies too big to meaningfully respond to user concerns.


@rkaplan Thanks for the response. I’ve downloaded Bookends to give it a test drive. Do you know if one can save the library file in iCloud rather than on the hard drive? It is defaulting to the hard drive but I’d rather save the library in iCloud IF AND ONLY IF this will not create a problem. Any experience with this?

iCloud sync between Mac and iOS is a specifically supported feature in Bookends – see

By the way, if you have an ISBN, you can use the magic wand button. Push the button, input the ISBN, and voila, the bibliographical information is added.

There are some helpful tutorial videos from a professsor Nicholas Cifuentes-Goodbody that are worth watching:

Thanks, I’ll check that out. I also found this very simple video on citing in Word. Got me up to speed very quickly. Thanks much!!

@iPersuade PS, one has to love a name like Nicholas Cifuentes-Goodbody! :slight_smile:

Thanks @rkaplan, that is good to know. I’m experimenting with both Bookends and Zotero. One issue I can’t figure out with Bookends, but that worked easily with Zotera, is importing information from Amazon. I’ll search for the answer (you’re not my tech support, :slight_smile: but it was surprisingly frustrating for a paid app vs a free one. I suspect that I’m missing something pretty easy but like I said, I’ll check it out. The book I was trying to import with Bookends without success is:

I tried “online search”, the Bookend browser, “Go to URL” and even dragging the URL into Bookends but nothing worked. All I got was this in Bookends:

Whereas in Zotero I got this: