I have recently been trying out Joplin as a replacement for Obsidian, as Obsidian is not open source and its sync options are, to be frank, terrible.

Problems with Sync in Obsidian.
The main problem I have with Obsidian is the sync feature, especially on devices that are part of different ecosystems. I mainly use four different operating systems these days: macOS, which is my main desktop OS, iPad OS and iOS, Windows on my gaming laptop, and eventually Linux, which will be on my Lenovo IdeaPad 1 when I send my Mac mini and MacBook Air back to Raylo.
Obsidian can only sync to iCloud or Obsidian Sync on iOS, which will work with Windows (via iCloud for Windows) and macOS; however, there is no iCloud client for Linux, so Obsidian just doesn’t work the way I want it to for my needs. Also, if I do change to my phone to Android in the future, Obsidian will not be able to sync to that either without Obsidian Sync.
Joplin can save the day?
Joplin, besides being fully open source, where as Obsidian isn’t, has a lot more options when syncing. It can use its own cloud system, Joplin Cloud, but can also use Nextcloud, Dropbox, a self-hosted version of Joplin Cloud called Joplin Server, as well as other cloud services.
I like to use my Nextcloud for all my syncing needs, as I have a robust backup solution in place for it already, and as I self-host the server, so my data doesn’t need to leave my network.
Joplin also supports all the major operating systems: macOS, Windows, Linux, iOS, iPad OS and Android. The app can sync between all of them without having to just use Joplin Sync, so for me, I use my Nextcloud Server.
Joplin’s File Structure.
Joplin uses Markdown, like Obsidian, to store its notes. However, unlike Obsidian, you can’t access the files directly like you can with Obsidian. Well, you can, but they will not make any sense as Joplin creates random file names for everything.
If you need to export your notes in a file structure that you can understand, it is very easy to do, so moving your data from one app to another is almost as easy as Obsidian.
What’s good about Joplin.
On the desktop, with the right plug-ins, I can do almost everything I did in Obsidian.
The major plus I think with Joplin on the desktop is that you can use external editors on the desktop, so for instance I am currently typing this out in iA Writer on my MacBook Air M1.
There are quite a few plugins available for Joplin. Some of the useful ones I have found so far include ones for journaling, templates, a plugin that makes Joplin show the same note every time you open the app, like a homepage, and a plugin to show word count and read time. There is not a plugin to publish your notes to WordPress, however, but there is one to publish to GitHub.
You can link notes together like you can in Obsidian, but I don’t think it is as intuitive as it is in Obsidian. The tagging system is about on par with Obsidian though there is nothing like Bases or custom properties of notes in Joplin.
What’s bad about Joplin.
While I really like the Desktop version of Joplin, the mobile version is nowhere near as good.
The plugin support is woeful; the Journaling plugin I stated above is not available in the mobile version, same with the homepage plugin.
The interface is also bad; you cannot customise it at all, so no side panels on the iPad, for instance, like you can with the Obsidian Mobile App.
Apple Intelligence, specifically the writing tools, also doesn’t work on the Mobile app at all, and on the desktop you have to use an external editor to use it.
While there are workarounds for the Journaling Plugin, there is no workaround for the homepage one at all, which I do like to use a lot on Obsidian as a daily reminder for what I need to do.
During my testing I also came across some bugs where the interface overlapped and sometimes I had to click on the interface twice to see my notes.
Am I going to switch to Joplin?
No. I really like the fact that it is open source. It can sync using my Nextcloud Server instead of iCloud. You can use external editors on the desktop and can do automatic backups of itself.
I also like the fact that, like Obsidian, it uses Markdown as its primary file type, but unlike Obsidian, you cannot directly access the file system itself due to the random nature of the file names. Exporting to a sensible file structure, however, is very easy.
The main letdown for me is the mobile app. While I am glad there is one, and the sync works really nicely, if it was a bit more customisable and supported a few plugins, then I would change in an instant.
However, since I use my iPad to type a lot of my blog posts out, I will have to try it for a bit longer to decide if I really miss the plugins that are not available on the mobile version.
Conclusion
I’ll be doing more testing but for now I’ll stick with Obsidian until the bugs are sorted out and the mobile app is much improved. I also prefer how Obsidian handles note properties and integrates with the bases feature which I use frequently.
Joplin is good if you need a basic note-taking app, but if you want more than just basic organisation, then I would say this app is not for you, unless you use an iPhone/iPad with a Linux desktop.
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