Mikael Mandron and Jordan Green scored late goals to send Gillingham through to the second round of the Carabao Cup.

Gillingham missed a golden early chance, had a penalty appeal turned down and a goal ruled out but in the final minute Mandron scored the opener and Green doubled the lead in stoppage-time.

Harris shuffled his side around for the cup tie, as much as he could with limited options. Five changes were made from the side which beat Rochdale in the league at the weekend.

The Gills were back at Plough Lane for the second time in nine days, having started their season with a disappointing 1-0 loss. The Dons included some of the key men from that performance, including midfield linchpin Paris Maghoma.

Neil Harris not only changed personnel but also formation, choosing to match up to the visitors wing-back set-up. Former Dons defender Cheye Alexander and David Tutonda came in to play on the flanks for Gills.

Gillingham had a great early opportunity to take the lead but after that the hosts took charge of the opening half. Striker Lewis Walker - who was on trial with Wimbledon before the season - put a shot wide with just the keeper to beat after Shaun Williams played him in with a fantastic ball forward.

It was the best moment of the half for the Gills. From then on Wimbledon grew in confidence, testing Jake Turner who was making his competitive debut for the visitors.

Turner comfortably dealt with a low shot from George Marsh but moments later spilled a powerful Will Nightingale effort and was grateful to see the ball drop just short of waiting striker Nathan Young-Coombes.

The Gills stopper had to save from Kyle Hudlin with his feet after Dons burst forward through Ayoub Assal after he had caught Alex MacDonald in possession on the halfway line. Turner also needed to be in the right place to deny Young-Coombes as he diverted a cross goalwards.

There were no changes at the break for the Gills and Nightingale headed an early corner narrowly wide for the hosts.

With an hour gone and Jordan Green off the bench, Gillingham began to turn the tide.

The Gills should have been awarded a penalty when David Tutonda was tripped in the box by Isaac Ogundere but referee Craig Hicks didn’t think so, much to the disbelief of the visiting bench.

Will Wright then went close with a free-kick that Nathan Broome had to turn away at full stretch.

As the game opened up, there were also a few incidents to keep the referee busy. One involved substitute Ben Reeves, moments after coming on. He was cautioned for a challenge as the home crowd called for a red.

Paul Kalambayi poked a close-range effort over the bar before the hosts had a penalty shout of their own when Assal went down under pressure from Alexander.

Gillingham thought they had taken the lead from Wright’s 77nd minute free-kick, the ball played into the penalty area and dropping for Mikael Mandron who stuck it in the net. Gills’ celebrations were for nothing as the linesman spotted a foul on the keeper and the referee awarded the free-kick.

Turner held onto a header from Jack Currie with five minutes left and Josh Davison put a great chance wide for the hosts as penalties loomed.

The tie was settled late on as Gillingham's substitutes struck. Mandron opened the scoring from the edge of the box on 90 minutes before Green danced his way to goal and struck a second from close-range to clinch the win.

Wimbledon: Broome, Nightingale, Kalambayi, Gunter, Ogundere (Fisher 80mins), Currie, Marsh (Bartley 90mins), Maghoma, Assal, Young-Coombes (Chislett 66mins), Hudlin (Davison 66mins). Subs: Tzanev, Sutcliffe, Adjei-Hersey, Bendle, Cosgrave.

Gillingham: Turner, Alexander, Tutonda (Law 84mins), Wright, Ehmer, Baggott, Williams (Reeves 66mins), Lee, MacDonald (Green 56mins), Kashket (Mandron 66mins), Walker. Subs: Morris, Akehurst, Gbode.

Attendance: 3,008 (325 away)