Makeshift striker Brain Howard struck the winner for Swindon as they earned their first league win of the season.
In a see-saw battle Swindon had to rely on goalkeeper Rhys Evans to save a second-half penalty before Howard stepped forward to steal three points for the home side.
MK Dons had the first real chance on goal after 20 minutes when Malvin Kamara got past his man to cross for Allan Smart. The former Watford striker somehow failed to connect with his header just six yards out.
The home side took full advantage minutes later when Sam Igoe curled a free-kick in from the right and found the head of Sam Parkin, who gave the home side the lead.
Goalkeeper Evans denied Smart midway through the first half before the visitors got themselves on level terms three minutes before the break.
Midielder Ben Harding saw his shot for kindly Smart, who made no mistake with a curling effort from the six yards.
Swindon came racing out the blocks after the interval and defender Sean O'Hanlon was unlucky with a header that was just inches wide from Igoe's cross.
Just seconds later another header, this time from Stefani Miglioranzi came back off the crossbar from a Howard corner.
Despite the home side's dominance MK Dons blew a golden chance to take the lead on the hour.
Defender David Duke was adjudged to pulled back Kamara and Dons striker Izale McLeod stepped forward to take the resulting penalty kick, only for keeper Evans to guess the right way and palm the ball to safety.
The visitors were punished two minutes later when Andrew Gurney's hopeful free-kick into the box fell kindly for Howard, who lashed it home from eight yards to give the home side the lead.
Evans was again called into action after 74 minutes when he clung on to Smart's back-post header following substitute Gareth Edds's cross.