Ben Reeves gave the Dons the lead in the first half after a mistake from Athletic goalkeeper Connor Ripley.
Despite a positive start to the second half, Karl Robinson’s men hit Athletic on the break and Kieran Agard nodded past Ripley to win the game for the Dons.
Manager Stephen Robinson elected to start the same team which came away with a respectable point against Charlton Athletic in midweek.
Latics started the game well and knocked the ball around with a lot of pace and energy.
Athletic forced a succession of corners in the opening exchanges of the game but the MK Dons stood resolutely and cleared the danger.
MK Dons winger Ryan Colclough received space on 13 minutes but defender Peter Clarke excellently got his body in front of the ball and shielded it out of play.
The first real chance of the game came midway through the first half as Ryan Flynn knocked the ball into the path of Freddie Ladapo who forced the goalkeeper to tip his effort over the crossbar.
MK Dons had their first chance of the game two minutes later as Kieran Agard managed to create space in the box but Clarke again was over to block the ball and clear the danger.
On the half hour mark, Latics had to be wary of a free kick which was awarded 25 yards out.
Reeves stood over the free kick but blazed over Connor Ripley’s crossbar as the danger passed.
One minute later, the goalkeeper had to be alert as he tipped a Nicky Marnard strike around the post which was heading for the bottom corner.
George Baldock found his way into the referee’s notebook on 34 minutes after a late challenge on Billy Mckay but a minute later, MK Dons took the lead.
Reeves received the ball 25 yards from goal and struck goalwards, Ripley managed to get a hand to it, but the ball went under his body and trickled into the bottom corner.
Four minutes after Baldock’s yellow card, he challenged Ryan McLaughlin on the left and the referee signalled a foul.
However, the full back fell to the ground clutching his hamstring and was taken off to be replaced by George Williams.
Colclough fired over before the end of the half and a late corner to Latics was defended well by MK Dons as Robinson’s men went into the second half behind.
He made two changes at half time as Lee Erwin and Charles Dunne came on to replace Ousmane Fane and Jamie Reckord.
Latics started the second half positively and were almost level soon after the break.
McLaughlin, who had a very good first half, won a corner on the right. Flynn found Clarke in the box who tried an acrobatic overhead kick but it rebounded off the crossbar and away from danger.
Latics were on top and McLaughlin was causing problems for the MK Dons defence, powering through the middle of the before the ball fell to Clarke who forced a smart save from David Martin in the Dons goal.
That hard work was undone on 55 minutes as Clarke was booked for a foul on Colclough and from the resulting free kick he delivered onto the head of Agard who made it 0-2.
Colclough and Maynard were the next to go close for the Dons but both their efforts went past Ripley’s far post.
Latics were struggling to make the ball stick in attack and the manager brought on Darius Osei in the place of Ladapo.
However, it would be MK Dons who again went closest to netting the next goal as Agard struck the crossbar from 12 yards.
The Dons dictated possession and Latics found it tough to break down the stubborn opposition.
Cameron Burgess had two headers which half tested the goalkeeper but it was the Dons that dominated and came away with all three points.
Oldham Athletic: Ripley, Dummigan, Clarke, Burgess, Reckord (Dunne 46’), Fane (Erwin 46’), Flynn, Green, McLaughlin, Mckay, Ladapo (Osei 68’).
Subs not used: Kettings, Law, Banks, Winchester.
MK Dons: Martin, Baldock (Williams 38’), Lewington, Walsh, Carruthers, Potter, Reeves (Bowditch 73’), Agard, Downing, Maynard, Colclough (Upson 89’)
Subs not used: Williams, Hendry, Nicholls, Tshimanaga.
Goals: Oldham Athletic 0-2 MK Dons (Reeves 36’, Agard 55’)
Attendance: 3,273 (193 visiting supporters)