I’m running Obsidian (flatpak, version 1.12.7) under MxLinux.
Under XFCE everything’s fine but under i3 Obidian is complaining about missing keyring (or similar). I’ve checked and gnome-keyring-daemon is running after boot.
Since I don’t want to store my secrets without cryptography, I’m using Obsidian only under XFCE. But this is not the best way to work (switching between i3 and XFCE).
Auto discovery is improved in Electron 42, but unfortunately Obsidian still uses 39 (which is de facto in “end of life” according to Electron team, I hope Obsidian team can update it soon).
If you can self-package Obsidian (definitely Flatpak isn’t designed for this), you can try to add --password-store=gnome-libsecret to the Electron that loads Obsidian’s app.asar.
Sorry, I didn’t explain well in my previous response. My for Gnome and KDE only meant for Gnome-like and KDE-like environment. In Electron repo docs, desktop environments that will be identified as gnome-keyring available are X-Cinnamon, Deepin, GNOME, Pantheon, XFCE, UKUI, and unity. This explains why XFCE works but not i3.