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He found an able ally in strike partner Billy Sharp who looked to be back to his best with a lively performance that saw him take his goal tally to 19 for the season.
MK Dons rarely looked happy and it was Portuguese keeper Ricardo Batista who kept the score down, while Craig Morgan battled well in desperate circumstances.
After forcing an early corner against a shaky looking Dons rearguard, Scunthorpe opened them up again to shoot into a third minute lead.
The ball was played in from the right by Jim Goodwin and striker Sharp found himself with oceans of space to head home beyond Batista who had no chance.
Looking well off the pace in the opening stages, Dons replied with a spectacular effort from Gareth Edds but he failed to trouble Tommy Evans.
The visitors fell further behind in the 10th minute from the penalty spot after Dave Partridge bundled Keogh over and Sharp cracked the ball home beyond the despairing Batista, who did manage to dive the right way.
That goal put Scunthorpe firmly in the driving seat but appeared to have done little to add drive to the game as it settled down to a steady pace.
Dons tightened up at the back and began to get forward a little more and Ben Harding fired in a solid shot from the left but failed to trouble Evans, followed up by a free-kick by Edds which beat the wall but not Evans.
The Dons' best chance came in the 59th minute. Substitute Filipe Morais did well to find Scott Taylor who got beyond Steve Foster but he only managed to drive his shot across the face of goal.