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Gillingham’s involvement in the Capital One Cup ended at the first hurdle on Tuesday night.
The Gills beat Bristol City in last season’s first round, when two divisions separated the sides, but the visitors, now in League 1, got their revenge with a goal in each half.
Sam Baldock put City ahead midway through the first half and Jordan Wynter added a second in the 65th minute.
Gills made five changes from the team which lost their League 1 opener against Colchester on Saturday. Callum Davies, Adebayo Akinfenwa, Bradley Dack, Antonio German and Michael Harriman were all brought into the team, while injury kept Charlie Allen and Matt Fish out of the squad - although Charlie Lee recovered from a bruised foot and started on the bench.
The visitors had plenty of the ball in the early stages and they took a 21st-minute lead.
Gillingham’s new signing Harriman – on loan from QPR to replace injured right-back Fish - was beaten in the area by Jay Emmanuel-Thomas and Baldock slotted the ball home as it was laid off to him inside the box.
The Gills should have levelled immediately. Joe Martin crossed the ball in from the left but Akinfenwa headed over. The striker headed a tougher chance over later in the half as Martin Allen’s men began to get a grip of the game.
Gillingham finished the half well, with Chris Whelpdale volleying an effort over, but City maintained their advantage at the interval.
They threatened to double their lead early in the second half, with keeper Stuart Nelson getting down to save from Baldock and then watching helplessly as Aden Flint glanced a free-kick an inch wide.
Nelson made a great reflex save to deny Brendan Moloney and the follow-up from Wynter was headed against the bar. The Gills survived another scare moments later when Moloney curled an effort wide with the home defence exposed once more.
With an hour gone Cody McDonald and Danny Kedwell joined the action in place of Akinfenwa and German, but it was City who found the net again just after the hour. Emmanuel-Thomas – a threat all evening - picked up the ball in space, smashed a shot at goal, and, after rebounding off defender Adam Barrett, the ball fell kindly for Wynter and he drilled home.
Myles Weston’s introduction gave City defenders more to think about as the Gills committed men forward in the latter stages. The winger gave right-back Moloney a run-around he didn’t need in the closing minutes, but a positive finish failed to produce the goals the Gills needed.
Gillingham: Nelson, Harriman, Martin, Barrett, Legge, Davies (Weston 65mins), Gregory, Dack, Whelpdale, Akinfenwa (Kedwell 59mins), German (McDonald 59mins). Subs not used: Lee, Howard, Butcher, Hare
Bristol City: Fielding, Moloney, Fontaine, Flint, Kilkenny (Reid 81mins), Baldock, Emmanuel-Thomas (Harewood 75mins), Wynter, Cunningham (Williams 86mins), Pack, Elliott. Subs not used: Wagstaff, Parish, Bryan, Taylor.
Attendance: 2,585.