When extracting annotations from PDFs in my Zotero library using the Zotero Integration plugins, links in the form of [p.2](zotero://open-pdf/library/items/84IYBUSS?page=2&annotation=RYXLUG63)are created for every annotation. In the past (can’t exactly say when, might have been months), clicking these links would take me to the appropriate annotation in the PDF in Zotero, but now nothing happens I click such a link.
Things I have tried
There is no message in the dev console when clicking a link. When clicking a mailto: link in Obsidian, it is correctly processed (opens Thunderbird’s compose message). When using xdg-open 'zotero://open-pdf/library/items/84IYBUSS?page=2&annotation=M4X2G7PW'in the terminal (Manjaro), Zotero also correctly opens, so the handler seems to be correctly set up. Also, to my knowledge, nothing substantial changed about my system setup.
SYSTEM INFO:
Obsidian version: v1.11.7
Installer version: v1.11.5
Operating system: #1 SMP PREEMPT_DYNAMIC Fri, 30 Jan 2026 23:06:21 +0000 6.18.8-1-MANJARO
Login status: not logged in
Language: en
Insider build toggle: off
Live preview: on
Base theme: adapt to system
Community theme: none
Snippets enabled: 0
Restricted mode: off
Plugins installed: 19
Plugins enabled: 15
1: Paste URL into selection v1.11.4
2: Tasks v7.22.0
3: Better Word Count v0.10.1
4: Auto Link Title v1.5.5
5: DB Folder v3.5.1
6: Dataview v0.5.68
7: Advanced Tables v0.22.1
8: Zotero Integration v3.2.1
9: Advanced Cursors v0.5.1
10: Templater v2.16.2
11: Full Calendar v0.10.7
12: Tomorrow’s Daily Note v1.4.0
13: Markwhen v0.0.7
14: Vault Changelog v1.2.0
15: Periodic Notes v0.0.17
RECOMMENDATIONS:
Community plugins: for bugs, please first try updating all your plugins to latest. If still not fixed, please try to make the issue happen in the Sandbox Vault or disable community plugins.
Also, I have disabled all community plugins, reloaded Obsidian and tried the link again - the problem persists.
If this did not help and Zotero links are still not working while other links do, then either:
Obsidian is using an incorrect link.
Obsidian may not have permission to open Zotero, although I’m not very familiar with Linux and unsure how this is handled there.
You could test this by right-clicking a Zotero link and opening it in your browser. If that works, the link itself is fine.
If you haven’t done so already, try if reinstalling Obsidian solves the issue.
I verified that the link is valid by copying it from obsidian into xdg-open, where it is correctly handled.
This sounds a bit vague to me. I don’t see at which point Obsidian should be disallowed, especially as it can open all the other programs that I use links for and since it used to work.
I reinstalled Obsidian but still encounter the same issue.
Opening the link in the browser correctly asks me if I want to open it in Zotero. But clicking “open link in default browser” on the link within Obsidian does nothing, whereas clicking a mailto: link does not open a browser but Thunderbird directly.
I now also looked into the opening schemes stored under .config/obsidian/obsidian.jsonand deleted the preferences for zotero (which were set to true) as well as the cache and restarted Obsidian. When I then clicked the link, I was again prompted if I want to follow it and if I want to save the preferences. I confirmed, but again, nothing happened afterwards.
After way too much time debugging with an LLM, I found the issue, and it’s indeed a Linux thing: The transient systemd unit launched Zotero with GDK_BACKEND=wayland, but it is an X11/XWayland application. I fixed it now by overriding the zotero.desktop handler with a wrapper script that unsets this variable.
This only affected Obsidian because it used a different environment than the command line environment that I ran xdg-open in.
I’m experiencing the same issue you described in your original post, could you please share the modifications you did to the zotero.desktop file to fix it?