Forward Bowditch has scored 48 goals in 227 appearances for MK Dons, helping them reach the Championship in 2014-15.
"I've enjoyed some fantastic memories during six years at MK Dons but all great things come to an end and it's time for a new challenge," he said.
The 30-year-old joins Darren Potter and David Martin in announcing their departure from Stadium MK.
Bowditch, who was out of contract in the summer, is the third long-serving MK Dons player to confirm their exit at the end of the campaign in the last week, while the future of the club's record appearance-maker Dean Lewington is also in doubt.
MK Dons chairman Pete Winkelman said of Bowditch: "Dean has been an important member of the squad for a long period of time and we will always be grateful for what he's done for the club."
Dean Bowditch will leave Milton Keynes Dons at the end of the season after six years at the League One club.