Obsidian and Zotero Integration

While working on a project recently, I realized I hadn't set up the Zotero Integration in Obsidian since moving to another computer. It's a nifty plugin that lets you pull references directly from Zotero and insert them into Obsidian, with little friction.

So I thought I'd take a few minutes to do that -- but, as is often the case, it turned out taking a lot more time than planned! I ran into some errors along the way.

A few quick notes in case I run into this again, or others perhaps find it useful.

The Zotero Integration plugin for Obsidian requires the GitHub - retorquere/zotero-better-bibtex: Make Zotero effective for us LaTeX holdouts | zotero-better-bibtex.

I already had Zotero installed via Flatpak, so I went ahead and installed the zotero-better-bibtex plugin, then the Zotero integration plugin.

But when I went to give it a go, I hit a snag: Obsidian opened a dialog box, hung for a moment, gave an error message, and then Zotero would crash. I tried this several times and got the same result each time. Very similar to the problem described at the Zotero Integration issue.

After a little googling, I double-checked that my Zotero port - which allows other apps to communicate with Zotero - was correct, and that it matched what the Obsidian plugin was looking for. All good.

After a bit more reading and poking, I decided it was probably a Flatpak issue with Zotero. I went to switch to the Tarball version of Zotero but found the instructions lacking. Ultimately, I found these instructions at the Fedora Project forums and they did the trick for getting the tarball installed.

One unaddressed issue I ran into: somehow, I wound up with a zotero.desktop file already present in my .local/share/applications folder. Deleting that was the last step I took to get the launcher working.

Switching to the tarball did take care of that error message, and Obsidian and Zotero were now communicating with each other. But when I tried to import anything, nothing ever got added to my documents. I would select the appropriate source and then, nothing.

What gives?

I hadn't added any citation formats!

This is a really easy step to overlook. As soon as I realized the error, I felt a bit foolish.

Before you can add a citation, you need to set up your citation formats via the settings window for the Obsidian plugin. For instance, in the screenshot below, I have two citation formats: one for a short note, using Chicago Style 17th edition, and one for the long note.

The name you give each format is important, as that is what will pop up in your command launcher. When I use the command launcher (ctrl+p on my machine) and search for Zotero, I should see commands with those names:

Choose your desired format from the launcher, and you'll then be prompted to find your source via the normal Zotero dialogue, similar to the connector with Word or LibreOffice.

The documentation for the plugin really doesn't discuss this process at all -- just hints at it via screenshots. I had totally forgotten this was required.

This integrates nicely with an Obsidian to Eleventy set-up.

Right now, I have the Zotero Integration plugin installed in the same vault I use to create notes for my digital garden. I can add citations directly to the post without leaving that app. And because I am using the Footnotes Shortcut plugin, I can add these easily to a footnote without missing a beat.^[1]

I don't use annotations or notes much in Zotero itself... but I wonder if you could use this sort of set-up to streamline an annotated bibliography?

---

1. For example, I generated this via Zotero without leaving the app, and put it in this footnote: MichaBrugger, “MichaBrugger/Obsidian-Footnotes,” TypeScript, June 13, 2025, https://github.com/MichaBrugger/obsidian-footnotes. Pretty nifty. ↩︎