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Gillingham lost a league game at home for the first time in five months on Thursday night.
Navid Nasseri scored on his first Gills start to cancel out Chuks Aneke’s opener for MK Dons.
But the Gills were dealt a late blow when George Williams netted a winner with three minutes left.
Nasseri was named in the starting XI for the first time as both Lee Martin (ill) and Callum Reilly (hamstring) missed out. There was no room in the squad for Josh Parker, who missed out last weekend on international duty.
It was Gillingham’s first home game since mid-February and they had plenty of possession in the opening half.
Jake Hessenthaler went close as he tried to lob the keeper and Nasseri fired well wide.
Gillingham were unable to turn their dominance into a goal and it was Aneke who put the visitors ahead with a controversial opener. Gillingham felt he used his hand to wriggle free of Gabriel Zakuani’s attention.
The MK Dons striker finished well after racing clear, putting his side ahead with 34 minutes gone.
Much of Gillingham’s play had been down the right side but it was left-sided man Bradley Garmston, who had strayed onto the opposite flank, who picked out Nasseri with a super cross. Lee Nicholls in the MK goal was beaten by a simple header.
The Gills dominated the start of the second half but it was home keeper Tomas Holy who had to be alert, saving well from Aneke as he tried his luck from the edge fo the box.
MK had appeals for a penalty when substitute Callum Brittain went down in the box, following a coming together with Connor Ogilvie, but referee John Busby booked the attacking player for a dive.
Gills’ leading scorer Tom Eaves was introduced with 20 minutes left.
Mark Byrne headed a chance wide for the hosts but Milton Keynes striker Aneke felt hard done by when pulled by by Gills defender Max Ehmer. The MK man looked to have got in on goal before being taken down but Mr Busby chose a yellow card instead of a red. Aneke hit the resulting free-kick over.
MK man Ed Upson was key to their goal, driving forward before picking out Williams and he tucked the ball away.
Gillingham: Holy, O'Neill, Ogilvie, Ehmer, Zakuani, Hessenthaler, Byrne, Wagstaff (Eaves 70mins), Nasseri (Nugent 90mins), Garmston, Wilkinson. Subs: Hadler, Lacey, Moussa, List, Nash.
MK Dons: Nicholls, Williams, Lewington, Wootton, Upson, Cisse, Aneke, Pawlett (Brittain 53mins), Agard (Thomas-Asante 77mins), Ward, Muirhead (Ebanks-Landell 74mins). Subs: Sietsma, Reo-Coker, Golbourne, Ugbo.
Attendance: 5,540 (443 away)