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…


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.


From the end users’ perspective, particularly mine, I feel there haven’t been many recent improvements. The change log is smaller in recent months. The roadmap looks the same since months. Features that have been requested for years are still (from what we can observe) not happening. They may be, but we have no way knowing.

While I can understand the mechanics of a major redesign, it feels as if offering new functionality in a smaller increments would show off progress to users more. Right now, all we have are promises.

Let’s also be honest, after such a major overhaul, the next iterations will focus on bug fixes, not new functionality, because things will break. Things that work fine today.

I agree releasing new features regularly in small increments should be the way to go. Actually, that’s exactly where we want to get. However, that’s not possible if your product is based on 2013 technology that is not supported anymore and for which you can’t hire any engineers.

I think we made solid technology decisions in 2013 which served us well over the years. But there was no React, no Node.js, no TypeScript - it was a different world that does not exist anymore.

So it was inevitable to rewrite everything at some point — which now is basically done and I will announce it here on the forum soon (actually very soon…).

And it’s not just a rewrite to get to the same state as before. Things will be significantly faster and streamlined and we’ve added many new features that address many longstanding requests from the forum.

You are right there will be some beta phase to catch bugs, but we’ll try to keep this short and intense. Going forward I’m very optimistic that we can do regular, more incremental feature releases. It’s not just more fun for you but also for our team. As I said before, I’m personally very excited about the whole Markdown and Note-taking topics.


Does that mean there will be public APIs since the refreshed Paperpile will be based on a more modern stack? I’m asking because that might ease pressure on the development team and external integrations could be built by the community.

If I can get the functionality I seek by rolling my own integrations rather than waiting, hoping, and waiting some more, I’d be more open to that now than, say, a year ago. I’d rather stick with Paperpile, do some development myself, than migrate. But I might do the latter if progress stalls (from what I’m looking for).

A public API is not yet in the cards for us, @hellstrom – below is my last update on the main thread about that topic.

Very intrigued by this upcoming update…any updates on ETA, what improvements to expect…?

Only discovered Paperpile today and I love what I see, but I’m torn between it and Zotero. It’s definitely much prettier than Zotero but the lack of full text search, seeing all annotations/notes sorted/organised in specified ways, annotation-specific tags, lack of Notion integration and hours of trying to get the Word plugin on my Mac working without success are what keep me on the fence. I’ll be following closely though and hope that development maintains a good pace. Cheers

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Welcome to our forum,! As @stefan mentions on this other thread, limited beta testing is set to start this month, with wider release expected before the end of the year. You can check out our roadmap to see what else is coming with this update.

W.r.t. our Word plugin not working properly, could you contact us via chat or email ( with more details of your experience, along with the plugin log file so the team can look into it? The easiest way to find the log is through the P icon on the computer taskbar > Preferences > Send Log File, then attach the paperpile-logs.txt file to your message.

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I have been using Paperpile for years, even before any Word plugin was available, and it has been the tool of my choice. I have been a PhD student now for 3 years, and Paperpile has been something that I used nearly every day. However, last months, it has been increasingly frustrating to work with Paperpile in Word. The amount of bugs occuring has been steadily increasing. Then each time is the same procedure of reinstalling the app, opening, closing. When I want to update the app, it often fails, when it is finally updated it, the app stills says it needs an update, and than the update fails, and than all this goes in circles. So I am thinking that if this won`t improve, I wil move to someting else. I understand that an occassional bug might occur, but I need a stable tool, that I can be sure works as it should.

Thanks for replying @vicente! I’m eagerly waiting for the beta.

My impressions of Paperpile and its team so far: Your active presence and transparency (+ @stefan ‘s) on this forum is a great sign and is appreciated. I love the content on the Paperpile blog too. I’m fully on board with your vision for what Paperpile is and should be, and I can tell it’s made by people who love+know what they’re doing and their target users. The experience of using what Paperpile currently has to offer has been excellent so far, it’s just a matter of fulfilling the roadmap. I see in the past you’ve struggled to ship promised features in a timely way which was worrying. But again, the active communication I’ve seen (+ the insightful explanation of the behind the scenes obstacles from stefan) make me more confident about the promised overhaul actually coming soon. I’ll be moving to an annual subscription as soon as the beta hits.

Best of luck with the launch, would love to help with feedback during the beta!


Welcome to our forum, @jzno! Thanks for reaching out here as well as via email. As I requested by that via, please share your Word plugin’s logs so the team can take a look and troubleshoot accordingly :pray:t4:

I was recently working on with Paperpile and linking Paperpile with (a note taking app that has block based editing features and backlinks etc) and Curvenote (another block based full featured scholarly writing tool that integrates bibtex). With both tools, using Paperpile for PDF annotation and immediate extraction of notes was wonderful. I do not think either Mendeley or Zotero does any better job than Paperpile on this aspect. There is no point of using any other tool than Paperpile if your use case is to store, retrieve, annotate PDF documents. If you work alongside something like or curvenote, or if you work in a browser like Vivaldi or Arc Internet Browser (this is still limited beta browser), Paperpile in its current state is a rockstar, is way more useful than many other reference managers. I do not personally like Paperpile’s too much reliance on Google Docs, etc, but that is their business decision, and I can live with it. I’d rather see a web enabled Paperpile desktop app, but that is not my decision, :slight_smile:

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@Arin_Basu Ah, I see we’re both fans of new and shiny macOS apps :wink:
I used for a while too, beautiful app. Ended up going back to Notion eventually because I wanted databases back to better manage the resources I save. And I’ve been using Arc browser for a few months now and it’s absolutely wonderful. Gamechanger. Huge fan of it.

And now the more I use Paperpile the more I love it. You’re right, Paperpile’s missing features aren’t as much of a dealbreaker as I thought they would be. Abstract search generally picks up most search queries, and I’m just saving + organising annotations/notes manually in a Notion page for each paper. Still would be nice to have better note-taking + organising but it’s overall a joy to use indeed.


Hello, this is Gulshan Negi
The decision to switch to another tool like Zotero or stick with Paperpile depends on finding the right balance between features, compatibility, cost, and user experience that best suits your specific requirements. It may be helpful to conduct thorough research, try different tools with your workflows, and carefully weigh the pros and cons before making a final decision. But I will suggest you to use Paperpile on behalf of my experience.

I wish I had these tools when I was a grad student. Back then there was only EndNote.

My ideal citation app would be a clean note with a side pane citation generator.

Research work should be simple, informal and organised.

Its results can be put to good use in a thesis or academic paper.