Goals from Keith Andrews, Danny Swailes and substitute Aaron Wilbraham's first for nine months condemned the Magpies to their first defeat of the season.
Milton Keynes started brightly and Jude Stirling's 25-yard left- foot curler flew just wide, before his long throw was somehow headed wide by the unmarked Drissa Diallo from eight yards early on.
At the other end, Dons goalkeeper Willy Gueret had an almighty let-off in the 14th minute when he escaped with just a yellow card for handling outside his box as County striker Lawrie Dudfield closed in.
And then Andrews put MK ahead four minutes before the break, just moments after Lloyd Dyer had been denied one-on-one by Magpies goalkeeper Kevin Pilkington.
Andrews stole in at the near post to head home Dean Lewington's inswinging corner from close range for his fourth goal of the season.
Dyer almost made it 2-0 on the stroke of half-time but his long-range drive flew just wide before Leon Knight's fierce angled drive was saved well by Pilkington soon after the re-start.
And the Dons' pressure told when Swailes doubled their lead in the 67th minute, stooping low at the near post to head in his first goal for the club from Lewington's corner.
The unmarked Dudfield wasted the visitors' only real chance of the game in the 75th minute when he headed substitute Spencer Weir-Daley's chip wide from ten yards.
Dons substitute Jemal Johnson curled just wide from 20 yards before Knight had a strong penalty appeal waved away eight minutes from the end after he appeared to have been brought down by Paul Mayo.
And substitute Wilbraham sealed the rout when he headed in Dyer's cross from close range five minutes from the end.