Darren Potter will depart Stadium MK when the current campaign comes to a close.
Chairman Pete Winkelman said: “Darren has been key to building an identity on the field and we will always appreciate what he’s done for MK Dons.
“He played an important role in promotion to the Championship as well as in some memorable victories over the past six years. We wish him all the best for the future.”
Potter said: “After six fantastic seasons, I'm sad to say that this will be my last at Milton Keynes Dons Football Club. I shall now be seeking a new challenge elsewhere.
“I will look back on my time here with great pride. As a Club, we’ve worked hard to form an identity on and off the pitch and play the game how we feel is the right way, sticking by our principles and believing in our style which brought us many great achievements!
“The promotion season was undoubtedly the highlight and no-one will ever forget the night we beat Manchester United 4-0 under the lights at Stadium MK in front of a full house! Those achievements will live long in the memory of us all connected to this Club!
“I would like to say a huge thank you to the fans, who have been nothing but fantastic to myself and my family during my time here.
“Also to my team mates and ex-team mates as well as all the staff and people who do so much for the Club.
“Finally to the chairman Pete Winkelman - it's been a great journey and I wish you all success for the future.”
Everyone at MK Dons would like to thank Darren for his immense contribution and wish him all the best in the future.