It was a win that no-one in the crowd of 3,819 could deny was merited for the hosts and ensured they have now picked up ten points from their last five games.
Their goals came from Sanchez Watt, Clinton Morrison and Freddie Sears, while a fourth clean sheet in the last five outings will have been welcomed at the other end of the pitch.
It was 0-0 at half-time, but Gillingham would have been the far happier with that scoreline.
Colchester bossed the play throughout the first 45 minutes and apart from a few early forays by former Witham Town player Cody McDonald, the Gills were kept on the back foot.
At the other end, the U’s made sure that Gillingham keeper Stuart Nelson had a busy opening spell.
Colchester posed threats on both flanks, but the link-up between Luke Garbutt and Sanchez Watt on the left was the most productive.
Garbutt celebrated signing an extension to his loan deal from Premier League side Everton with a superb display.
He was central to everything that Colchester did well in the first half and it was from one of his shots that they had the best chance before the break when Nelson parried a fierce effort to Craig Eastmond, but he couldn’t control the rebound and his snap shot was off target with the goal gaping.
Perhaps the only criticism that could be thrown at the hosts was that they hadn’t finished off some of their chances, but it didn’t take them long to set that record straight after the interval.
The U’s pounced on a 50th minute error in midfield and broke with pace and precision, before Watt ended it by slamming the ball home for a deserved lead.
Marcus Bean, Dominic Vose and Brian Wilson had all been instrumental in the move and it heralded a further spell of home domination.
Colchester drove forward with increasing confidence and with Vose producing more and more threat off the right flank, it appeared only a matter of time before they got a second.
Vose curled a lovely effort just over and Garbutt tested Nelson with a low shot, but Colchester were unable to forge the second goal that their play deserved.
That was the case until the 85th minute when a free-kick by Garbutt came back to Watt on the edge of the box and his drilled shot was deflected into the net by Morrison’s deft touch.
It allowed Colchester to see the game out with comfort and gave the scoreline a little bit more of the look that their play had merited.
And Sears, making only his second appearance since late October, ensured their dominance was really reflected as he struck in injury time from 25 yards to make it 3-0.