Bradford, who face Sunderland in the FA Cup fifth round on Sunday after seeing off Chelsea in round four, had to come from behind at Valley Parade with goals from the recalled Billy Clarke and James Hanson.
MK Dons’ £5m man Dele Alli put Karl Robinson’s men ahead early in the second half, but after soaking up plenty of Bradford pressure the visitors succumbed to two goals in the space of 14 minutes.
Bradford dominated the territory and corner count in the first half but only had a couple of scuffed efforts to show for their dominance.
They also started the second half in a similar manner – on the front foot – forcing MK Dons to back pedal, but it was the division’s top-scoring visitors who broke the deadlock through Alli.
The Tottenham-bound teenager cooly finished through Jordan Pickford’s legs on 54 minutes after the Bradford keeper fluffed his low clearance to Johnson Clarke-Harris.
Bradford were level though two minutes later though when Filipe Morais’ centre was headed out to Gary Liddle, who headed the ball back into the box and there was Clarke to beat the offside trap to fire home.
And with 20 minutes remaining Hanson fired the Bantams into the lead after Jon Stead had controversially controlled the ball with his hand.
Stead collected the ball, which appeared to hit his arm, before turning inside to slip Hanson into the channel and the big striker then won the race with his defender before clipping the ball home.
Andrew Davies wasted a fine chance to make it 3-1 when he scooped over from inside the six-yard box after Hanson’s superb knockdown.
Carl Baker, who had fired wide minutes earlier, had a great chance to equalise for MK Dons when he surged into the box, but Pickford denied him with a brilliant low stop as Bradford earned their first league win in 2015.