MK Dons kept alive their hopes of automatic promotion with their 12th away win of the season.
Jason Puncheon went close before his team got the game's only goal when Luke Chadwick pounced on a mistake by Scunthorpe skipper Cliff Byrne.
Scunthorpe's best effort in reply came from a free-kick by Grant McCann which was tipped over by keeper Willy Gueret.
The home side offered more later on, and Gary Hooper thought he had a goal, but it was ruled out for offside.
Scunthorpe: Murphy, Wright, Byrne, Mirfin, Mills, Lansbury (Pearce 90), Trotter (Sparrow 69), McCann, Woolford (May 57), Hayes, Hooper. Subs Not Used: Lillis, Hurst
Booked: Hayes.
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Milton Keynes Dons: Gueret, Regan, O'Hanlon, Llera, Lewington, Wright (Cummings 86), Gleeson, Puncheon, Howell, Chadwick (Baldock 71), Gerba (Flo 79). Subs Not Used: Abbey, Navarro
Booked: Chadwick, Gueret, Baldock, O'Hanlon
Goals: Chadwick 35
Att: 4,873
Ref: Anthony Taylor (Greater Manchester)
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