Published: 16:40, 17 December 2016
A third straight home win for Gillingham lifted them into the top half of League 1.
The Gills were thankful to goalkeeper Stuart Nelson for saving Dean Bowditch’s first-half penalty.
Cody McDonald headed the home side in front in the 72nd minute to win it.
Gills were looking to bounce back from a 4-0 defeat to Bolton, in their last League 1 outing, a game where they were outclassed by their hosts.
In contrast, their last home match had seen them beat Rochdale 3-0.
Justin Edinburgh’s side were unchanged from the one that started against Bolton and they saw plenty of the ball in the opening half, with much of their attacking play going through Jay Emmanuel-Thomas.
Bradley Dack came close for the Gills early on, but his effort was hooked off the line by defender Dean Lewington.
Samir Carruthers curled a free-kick just wide for the visitors, but MK were being let down by some poor finishing.
McDonald almost broke free for the Gills but he was adjudged to have fouled the MK defender in the process, earning the striker a booking, most likely for dissent rather than the challenge.
Scott Wagstaff and Paul Konchesky were also cautioned. Referee Brett Huxtable further infuriated the home crowd when he pointed to the spot at the end of the first half.
Konchesky was adjudged to have pushed Kieran Agard over, but Nelson saved with his legs as Bowditch went straight down the middle.
There was a lack of goal action at the start of the second half, with MK’s Ben Reeves going the closest, shooting wide with the aid of a deflection.
With an hour gone the Gills forced David Martin into a save. Baily Cargill’s downward header from Dack’s corner was stopped on the line.
Frank Nouble also tested Martin, his low shot from 20 yards gathered again by the keeper. The left-sided forward also won a 72nd-minute corner following a run started in his own half and that move led to Gills’ opener.
Dack’s corner was played short and his eventual ball into the box was headed home by McDonald for his seventh goal of the season.
Jack Hendry almost gifted the Gills a second, losing possession in a dangerous area, but the finish from Josh Wright wasn’t good enough to beat Martin.
Carruthers lashed a shot over at the other end as the Gills kept the visitors out.
Gillingham: Nelson, Wagstaff, Konchesky, Cargill, Ehmer, Hessenthaler, Wright, Dack, McDonald, Nouble (Jackson 80mins), Emmanuel-Thomas. Subs not used: Hadler, Oshilaja, Donnelly, Oldaker, Cundle, Byrne
MK Dons: Martin, Baldock (Hendry 54mins), Lewington, Upson, Carruthers, Potter, Bowditch (Maynard 64mins), Reeves, G B Williams, Agard (Colclough 80mins), Downing. Subs not used: Nicholls, G C Williams, Powell, Aneke.
Attendance: 5,682 (350 away).