The 27-year-old was a regular for Boro in 2011/12 as they secured the last play-off place in League One.
Dons' first-team coach Simon Bassey is delighted with the coup, highlighting Long's experience as a major benefit.
"Stacy gives us that bit of experience," Bassey told AFC Wimbledon's official website. "He is a very talented footballer who will add craft to our midfield. He has a winning attitude as he has helped Stevenage to promotions. Hopefully his experience will rub off on the younger players we have here and we can do what Stevenage have done."
The Dons attempted to sign the midfielder three years ago when he left Ebbsfleet. A deal did not materialise back then, but Long said: "I have always felt there was interest in me from AFC Wimbledon.
"That was a key part in my decision to sign. It is nice to come to a place where you feel wanted and hopefully I can put my own stamp on the team and help the club do better than last season."
