Short answer

Yes. The official FAQ confirms that Active Matter works on Steam Deck, has native Linux support, and supports controllers on PC.

Confirmed platform support

Question Official answer
Does it work on Steam Deck? Yes.
Is there native Linux support? Yes.
Are PC controllers supported? Yes.

What support does not guarantee

Official support does not promise one fixed frame rate, graphics preset, battery-life result or control layout for every device. Performance can change with hardware, operating-system updates, game patches and graphics settings.

Use the current client defaults first, then lower demanding graphics options if performance is unstable. Check System Requirements before comparing a desktop Linux system with a handheld.

Steam Deck and cross-platform play

Steam Deck support is a device-compatibility question. Crossplay and progress sharing are separate features. See Crossplay for the current platform and cross-progression rules.