Mark Robins saw his side come away with only a solitary point following a dominant display at Priestfield.
The Sky Blues came into the fixture following a disappointing performance and result away at Blackpool in the week and Robins was quick to highlight how pleased he was with his team's reaction: "I enjoyed watching us, the only thing is that it began to get frustrating when we weren't taking our second chances.
"But it was better. We have moved the ball well and created decent openings and they [Gillingham] have had a really decent start to the season, especially on their own patch.
"On the back of the result from the other day, we obviously worked on things on Thursday and Friday and spoke about what we need to do as a team to keep our identity, not get away from that and believe in it.
"I am really pleased with them and proud of them because they have gone in and been brave, but again just lost a little bit of energy towards the end of the game as you do.
"Reise Allassani came on and lifted us again, almost got in and created one or two bits of mayhem for them. Jordan Ponticelli came on and had a bit of a cameo there and we looked a threat all day.
"Pleased with the performance but slightly disappointed on the outcome."
Jonson Clarke-Harris initially put the Sky Blues in front only 20 seconds into the second half and Robins was quick to praise the striker: "He was good, really good, and that is the standard that I now want from him. If he does that then he is the best target man at the club bar none.
"He's a threat, he's a real threat and that was a really good performance from him today and the standard is now set."
Despite only finding the back of the net just once throughout the afternoon, the Sky Blues put the Gills defence under pressure for the entirety of the match by having 20+ efforts on goal, and the City manager said that his side were only one goal away from making it a rout at Priestfield: "If we got the second goal we could have got a third and a fourth and it could have been a rout because we were controlling the game.
"Today for us was about trying to put right things that were wrong on Tuesday night. So I am pleased because they have taken it on board and I am pleased that they've done that. Today was a lot, lot better, and we just need to be a bit more ruthless."