Lewington, whose 11th season with the club culminated in promotion to the Championship for the first time in the Dons’ short history, has put pen to paper on a two-year deal.
The 31-year-old left-back said: “I’m extremely happy to be staying. I’ve always loved it here and always been really happy. It’s been a great partnership.
“Next season there will be a lot of big teams and a lot of top-class grounds – we are all very excited about next season.”
Former Wimbledon trainee Lewington enjoyed a testimonial fixture against Nottingham Forest last summer and during the 2014/15 campaign he made his 500th appearance for MK Dons – the only player in the club’s history to reach the milestone.