They return as enemies in Lets-a-go, Mario. They attack like they did in Super Mario 64, spitting fireballs at the heroes. When hit from below, they fall down onto their heads and become vulnerable. Then they are vulnerable to everything, including being run at from the side. They can even be stomped on when they're flying - doing so results in a large Spin Jump similar to the effects of jumping off of a Spindrift. However, they are always too high to stomp on without hacking.
Fly Guys appear as common enemies in this game. There are two types of general Fly Guy behavior: some idly fly around a specific area before spitting fire at the player, a la Super Mario 64. The other type of Fly Guys only appear in rows. If Pokey manages to take out all of the Fly Guys in a row with one segment, he will be awarded a yellow Sphere.