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Kickoff had to be delayed by 15 minutes because of the number of fans that turned up to see the match, with the official attendance topping 27,000.
The home side made a perfect start on their return to the stadium, as new signing Frank Nouble burst into the box before squeezing the ball under the keeper to break the deadlock inside 10 minutes.
Gillingham made a bright start to the second half as they looked to get back on level terms, with Kortney Hause attempting to head in from a Jake Hessenthaler corner, but his finish was a fraction high.
Luke Norris came off the bench late on and created a couple of chances, but was unable to test Allsop again.
Jim O'Brien almost put the result beyond doubt inside the final 10 minutes with a volleyed effort from the edge of the box, but his shot was watched all the way.
The result lifts Coventry up to eighth in the League One table, while Gillingham sit 14th.