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@asynec It depends what program you're opening the invite links from. Firefox will prompt you by default. Chromium will use xdg-open. I don't know about other programs. Here's how to check what xdg-open is currently configured to use for all the schemes that Zoom recognizes:

xdg-mime query default x-scheme-handler/zoommtg
xdg-mime query default x-scheme-handler/zoomus
xdg-mime query default x-scheme-handler/tel
xdg-mime query default x-scheme-handler/callto
xdg-mime query default x-scheme-handler/zoomphonecall

If you would like to change them all to open under Firejail, here's how:

xdg-mime default ZoomFirejail.desktop x-scheme-handler/zoommtg
xdg-mime default ZoomFirejail.desktop x-scheme-handler/zoomus
xdg-mime default ZoomFirejail.desktop x-scheme-handler/tel
xdg-mime default ZoomFirejail.desktop x-scheme-handler/callto
xdg-mime default ZoomFirejail.desktop x-scheme-handler/zoomphonecall

Please let me know if that resolves your issue. If it does, I'll add a post-install script to print out additional instructions.

How can I associate Zoom links with Zoom-Firejail instead of the regular Zoom? By default, my cal invites are still opening in the unsafe version of Zoom.

@hockdudu I'm unable to reproduce the issue under fish. What is /bin/sh symlinked to on your system?

I use fish as my shell and I got this error:

fish: Unknown command: --
fish:
--
^

Replacing this line in zoom-firejail solved my problem.

-/usr/bin/firejail -- zoom "$@"
+/usr/bin/firejail zoom "$@"