The Problem

This is a problem I've had ever since I first used GNOME 3, now GNOME 40, around a year ago. For some reason unknown to me, GNOME would ignore my custom keybindings that I had set up in the GNOME settings. My changes were binding Super+1 to switch to workspace 1, Super+2 to workspace 2, and so on.

This works some times, but often it would fail and execute the default actions on those shortcuts. The default actions for Super+N (where N is a number) is to launch the Nth application in the favorites bar. I tried to find a fix for this a long time ago, without success. Just a few days ago, I've finally had enough of this and started looking for a solution again.

Dconf and the Solution

After some reading, I found out about dconf. Quoting from the GNOME wiki about dconf:

dconf is a low-level configuration system. Its main purpose is to provide a backend to GSettings on platforms that don't already have configuration storage systems. dconf is a simple key-based configuration system. Keys exist in an unstructured database (but it is intended that keys that logically belong together are grouped together).

So dconf is basically a settings configurator for GNOME. The configuration for some of the actions of the GNOME shell is contained here. The frontend for dconf is gsettings. Using this, the default keybinding actions can be changed. To list the default keybindings, use this command.

$ gsettings list-recursively org.gnome.shell.keybindings
org.gnome.shell.keybindings switch-to-application-4 @as ['<Super>4']
org.gnome.shell.keybindings switch-to-application-7 ['<Super>7']
org.gnome.shell.keybindings toggle-message-tray ['<Super>v', '<Super>m']
org.gnome.shell.keybindings toggle-application-view ['<Super>a']
org.gnome.shell.keybindings focus-active-notification ['<Super>n']
org.gnome.shell.keybindings switch-to-application-2 @as ['<Super>2']
org.gnome.shell.keybindings switch-to-application-5 @as ['<Super>5']
...

There you can see the value of switch-to-application-4 is ['<Super>4']. This is the default action of the shortcut Super+4. Now, to make GNOME follow only the keybindings set through the GNOME settings, we just have to change the value of the action to an empty list []. Here's the command to do so:

$ gsettings set org.gnome.shell.keybindings switch-to-application-4 []

To change the bindings for N workspaces, you can use a for loop:

$ # N is 6 in this case
$ for i in {1..6}; do \
>   gsettings set org.gnome.shell.keybindings "switch-to-application-$i"; \
> done

Conclusion

Done! just around half an hour of googling led to this. Just a few commands to fix a problem that has been annoying me for a long time. To those reading with the same problem, hope this helps!