The talented central defender has been plagued by groin problems since the back end of last season and his original comeback against Chelsea at the end of October was aborted at half-time when the injury re-surfaced.
However, he looked in fine fettle against the Dons alongside Anthony Gardner and now hopes to press on with his season.
"It was quite hard being my first game back and it was pleasing to get 90 minutes under my belt after being out for so long," reflected Alton, who made his first team debut against Liverpool at the Lane the season before last.
"I felt it in the last couple of minutes of the the half against Chelsea and, as a precaution, I stayed in. It did prove to be a problem, but at the moment I'm feeling good and it is just nice to be playing again."
Alton reasons that with nagging injuries it is vital to remain mentally strong and have the belief that a return is in sight.
"It does get you down because you just want to play. Originally, when I got the injury, I thought it would just be a couple of months and I'd be back.
"To come back training and not be right, then come back again and not be right does get you down.
"You've just got to try and stay mentally strong and know that you are going to get better eventually. But it is hard.
"I feel alright at the moment. Normally it would be aching a bit after the game but I feel quite good."
Alton Thelwell is hoping that his injury troubles are behind him after coming through a full game for the reserves against Wimbledon on Monday.