Flanagan, who came through the academy ranks in Milton Keynes, has put pen to paper on a one-year deal to ensure he will be with the Dons for their maiden Championship campaign next season.
The 23-year-old centre-back told the club’s official website: “I’m more excited to be staying than ever after the promotion.
“Kyle (Kyle McFadzean) and Kaysy (Anthony Kay) did brilliantly last season and that probably hindered my opportunities, but I felt I did well when I came in and I’m buzzing for next season.
“I’ve been working hard in the off-season and I want to come back flying.”
Since making his Dons debut as an 18-year-old at Carlisle in 2010, Flanagan has made almost 50 first-team appearances for the Dons.
MK manager Robinson said: “Tom is one for the future and I do think he has a great future at this football club. His opportunities were limited last season because the other players did so well but when he was called upon he was magnificent.”