The 25-year-old played 65 minutes as an over-age player when Wanderers' Under-21 side played out an entertaining 3-3 draw with Manchester City at Euan Fields.
Wheater ruptured his anterior cruciate ligament last May and has not featured in Bolton's Championship campaign this season.
"It's tremendous to be back," he told the club's official website. "It's great to get all of the running and getting fit out of the way so I could be back out on the pitch again.
"The game went really well for me, as good as I could expect. Obviously I'm not 100 percent as I only played 65 minutes, but I felt good. Hopefully I'll play more next time."
He added: "I think I'll need a bit more time to get sharp but I didn't feel any pain in my knee. It's more an issue of concentration and getting back to remembering where runners go. All I've been doing is running for the last month or so."