I had to deal with this when making my own Qubes theme. The only decent workaround I could find was adding a background layer behind each icon you want to fix, which is what the original post is explaining. However, renehoj is explaining how to do it for SVG/vector images, but your icons might be PNG/raster. Here’s what you need to do:
- Locate the icon. You can usually find all installed system themes in /usr/share/icons. Programs bundled with their own icons usually show up in /usr/share/icons/hicolor (such as Network Manager). You can also ask AI to quickly research the source code of some programs and give you the name of the icon.
- Figure out the specific icon size the system tray is using. Themes have the ability to swap icons depending on the desired size. This is usually used to perfect antialiasing/readability on raster themes. For your case, you only want to add a background to the specific size icon the tray uses, so it doesn’t affect the icon if it shows up at different sizes. (It’s usually 16x16 or the closest to 16x16 by the way.)
- If the icon is PNG, open it in an image editor of your choice and put a background layer behind it which is the same color as your taskbar. If it’s SVG, you can probably follow what renehoj said.
- (OPTIONAL) If you want your icon to be monochrome instead of being colored by the Qube, set your Qube color to gray for good results on dark theme taskbars.
- Replace (or add if the icon was in hicolor) the specific icon in your active theme with the one that you just made. Make sure it’s the correct size. Keep in mind that most AppVMs use root directories from the template, so you might need to copy the theme to your user directories (and apply it) if you want it to be permanent.
- Reboot/restart program and it should work.
Also for the people asking about modifying the Whonix icon, copy your icons to the Whonix Gateway like any other VM and use " qvm-run -u root whonix-gateway-18 ‘pcmanfm-qt’ " to open an administrator file explorer.

