Should I stay or should I go?

I hope this post is not in violation of community rules or taken as an attack on the developers (it is not). I was one of the earliest users of Paperpile and have been a huge fan/supporter of the platform ever since. However, my personal move towards plain text (markdown) workflows and personal knowledge management (PKM) software has been increasingly frustrated by the limitations of Paperpile. I know they are aware of these issues and are working towards mitigating some of them, but the slow pace of development and recent improvements to Zotero — as well as new plugins for Obsidian and Logseq — have me reconsidering my choices. I hope my thoughts on this matter will provide a useful (and civil) discussion about this issue.

Here is a list of what is already possible if I were to switch to Zotero for working with PKMs

Some additional benefits of Zotero

  • ability to collaborate with students who are using free accounts (PP’s academic pricing is very generous, but still more than many students are willing/able to pay.)
  • ability to save webpage snapshots directly in Zotero
  • better support for working in plaintext writing programs such as Ulysses and Zettlr
  • ability to annotate PDFs without making permanent changes to original file

I still greatly prefer the Paperpile user interface/experience - it is just a much more elegant app. And the cost of storing several thousand PDFs in Google is much cheaper than Zotero’s paid storage solution (especially with the academic discount). But as my workflow has changes I’m just not sure that PP is still right for me? Would like to hear what other people think. Has anyone switched to Zotero and then come back? If so, why?

This is related to several other posts on the forum, including: Logseq plugin supports Paperpile BibTeX, URL Scheme with Citekey, Roam / Obsidian Academic Workflows, Survey and Roadmap for LaTeX / Markdown / Overleaf :white_check_mark:


UPDATE: After writing this I decided that I should just try it for myself, so I will keep my PP account active but primarily use Zotero for the next academic year and see how I like it. In the meantime hopefully PP will release the long awaited changes and I can see how they compare when they come out. Happy to report back then.


I’ve had the sense for a while that PP’s medium/long term viability will hinge around integration with PKMs rather than almost any other feature, current or planned. @Kerim’s post seems to corroborate this sense. PKMs present a paradigm change in how we do academic workflows, and despite their openness, quickly become the center of gravity of how we do things.

It is unfortunate that the re-write is taking so much bandwidth that any other features (even ones that are admittedly easier to implement) are taking a back seat.

Even more so because, due to its web first and ability to link to citations, PP started off with an immense advantage over almost all other platforms. I personally think it still retains its advantage at the moment however likely not for long, esp if another year passes with no progress on PKM integrations.


Hi Kerim - it seems the problem is mainly the lack of Paperpile’s support for PKM’s and Markdown. If that’s the focus of your workflow I can see why you are considering alternatives.

We are here for the long run, and I’m convinced Paperpile will be the best alternative also for those workflows eventually.

Unfortunately, it will take more time until we get to Markdown, note taking and integration with PKMs.

The reason is – pretty much as always – that we are busy working on other features. Features, other users are waiting for…

Later this year, you will see one of the biggest updates we’ve made to Paperpile yet. It’s a complete rewrite that will address dozens of longstanding feature requests here in this forum. It will change our roadmap dramatically as we finally can tick of so many “must haves” from the past and it seems Note taking and Markdown will end up near the top after that…

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I think this is a fair assessment. After switching I am already 90% towards where I wanted to be with a plain text workflow, and I believe that most of the remaining roadblocks will be ironed out by the end of the year. Whereas it sounds like it might be at least another year after that before similar features are available in Paperpile. When you are ready to start working on those features I will be happy to share my thoughts if they might be of help.

Thanks @stefan for engaging on this thread. It’s great to hear that the delays are not a precursor for lack of interest in long term development of the platform and that you all ‘are here for the long run’.

Like Kerim, I can’t overemphasize the need to allow PP to connect to PKMs. Except for Zotero, PP is probably the best platform poised to do so (and Zotero has QOL issues of its own). You all have done a terrific job with the automated BibTex export. I think it provides a great base to facilitate PKM integration. I can already ‘connect’ my Obsidian vault to paperpile using that export workflow. Unfortunately the current export does not add a link to the pdf- this should not be hard to do and would address a major pain point.

You also have an excellent annotation export to MD functionality in your PDF reader- however, it requires a lot of clicks to access and is not automated. If that can be exposed as an automated export similar to your current BibTex export workflow, you would likely be 90% of your way to providing PKM integration.

I fully agree. I am embarking on a PhD and the ability to take connected notes is of huge importance. I currently use Obsidian for all my literature notes, and am looking at Scrintal (new product in closed beta) for its ability to integrate PKM style note taking with visual organisation (mind-map-esque).

I did recently write a paper in Overleaf since I discovered that integration combined with my institutional account works quite well, and LaTeX isn’t too hard to pick up the basics…however, this doesn’t work for general note-taking.

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