The 29-year-old former Billericay, Peterborough United and Gillingham man scored nine goals in 24 appearances for Boro last season.
"There were a couple of players at Stevenage that stood out last season and Chris was one of them," Dons boss Neal Ardley told the club website.
"His goalscoring record from midfield has been exceptional over the years."
Whelpdale becomes AFC Wimbledon's third signing of the summer following their promotion to the third tier via the League Two play-offs.
The Dons have not disclosed the length of his contract at Kingsmeadow.
Find all the latest football transfers on our dedicated page.
League One side AFC Wimbledon have signed Chris Whelpdale following the winger's departure from Stevenage.