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Defender Ryan Jackson scored one and created another as the Gills maintained their perfect start to the season.
Jackson’s early goal was all that separated the sides during an entertaining first half.
Gills doubled their lead just before the hour, with Antony Kay turning in Jackson’s cross past his own keeper, before Tom Pope headed home for the visitors.
Victory means it’s three wins from three in all competitions so far for Justin Edinburgh’s men.
Manager Edinburgh named new signing Jamie O’Hara on the bench but, as expected, was without Bradley Dack (knee) and Max Ehmer (concussion).
Josh Pask started his first game for the Gills, replacing Ehmer in central defence.
Pask impressed with some timely interventions after Gills’ opener, showing a cool head as Bury threatened.
Gillingham had taken the lead in the sixth minute as Jackson fended off the attention of Nicky Clark, latching onto Mark Byrne’s through ball, before finishing well past keeper Ben Williams.
Gillingham were unable to build on the goal, allowing Bury to create numerous openings, with some dangerous crosses going into the box.
Deji Oshilaja made a last-ditch challenge on the edge of the box to deny Hallam Hope and the same player almost got on the end of a low defence-splitting pass.
Gillingham ended the half the stronger, however, and visiting defender Nathan Cameron twice had to use his strength to keep them at bay. He outmuscled Cody McDonald when he looked to get onto the end of a Billy Knott ball over the top and then the big defender made a challenge on Josh Wright as he attempted to pounce on a cross.
Emmanuel Osadebe thumped a header onto the bar from a Paul Konchesky cross and Wright’s 25 yard volley was saved, leaving Gillingham with just the one goal advantage at the break.
Neither keeper was tested in the opening stages of the second half. Bury’s double change at the break failed to turn the match in their favour.
It was their captain, defender Kay, who turned a Jackson cross into his own net in the 58 minute to double Gillingham’s advantage.
Bury chances either side of that goal had both gone wide, with Top Pope blazing a chance over from an angle. Substitute Zeli Ismail put an effort the wrong side of the post.
The visitors halved the deficit with 66 minutes gone. Bury broke down the left and Konchesky was unable to get back to stop a cross from Tom Soares which was headed home by Pope.
There were a few nervy moments towards the end of the game. Substitute Rory Donnelly hacked clear one attack and Jackson needed to block another effort as Bury looked to level the scores.
Late substitute Joe Quigley fired over for the Gills and then stumbled in the box during stoppage-time after Wright picked him out with a super pass.
Gillingham: Nelson, Jackson, Konchesky, Pask, Wright, Byrne, Oshilaja, Knott (Hessenthaler 78mins), Osadebe, McDonald (Quigley 86mins), Emmanuel-Thomas (Donnelly 78mins). Subs not used: Hadler, O’Hara, Oldaker, Dickenson.
Bury: Williams, Jones (Maher 70mins), Leigh, Kay, Clark, Danns, Mellis, Soares, Hope, Cameron, Pope. Subs not used: Rachubka, Etuhu, Dudley, Bedeau.
Attendance: 5,324 (189 away)