The Dons' leading marksman Dean Bowditch fired the visitors into an 11th-minute lead with his 13th goal of the season, sweeping a first time shot past goalkeeper Sam Slocombe after fellow striker Charlie McDonald had got behind the home defence to pull back a low cross from the right.
It was only the second goal conceded in six games by Scunthorpe, who continued to struggle as an attacking force in the second half and it was MK Dons who made it 2-0 after 54 minutes with McDonald again the provider for midfielder Daniel Powell to force his shot home from close range at the near post.
McDonald also went close to getting on the scoresheet himself with a shot which was well saved by Slocombe.
A miserable afternoon for Scunthorpe was compounded after 72 minutes when they were reduced to 10 men following a controversial red card for striker Jordan Robertson, sent off for his challenge on Dons' centre back Gary Mackenzie following the intervention of the fourth official.
Dons midfielder Shaun Williams made it 3-0 with a well-struck shot from long range five minutes from time.