The visitors bossed the first half and winger Jason Puncheon went close with an angled drive that was beaten away by goalkeeper Joe Murphy.
It was no real surprise when MK Dons went in front in the 35th minute following a good finish from midfield man Luke Chadwick.
He broke unmarked into the box and clipped his shot past Murphy after a mistake by Scunthorpe skipper Cliff Byrne.
Scunthorpe's front two of Gary Hooper and Paul Hayes, who have netted 48 goals between them this season, struggled to make an impression.
It was midfield man Grant McCann who went closest with a cracking free-kick which was tipped over the bar by keeper Willy Gueret.
Early in the second half, Mark Wright could have doubled the visitors' lead only to be denied by a good save from Murphy.
Scunthorpe did have the ball in the net after 61 minutes with a close-range header from Hooper but it was flagged offside.
Full-back Andy Wright almost scrambled an equaliser for the home side with an angled shot which Gueret just managed to keep out.
The French keeper rescued the visitors again in the closing stages when he made a great block to keep out a shot from Hooper, who had for once wriggled through the Dons defence in which Sean O'Hanlon was an outstanding figure.