Goals from Harriott and Stevenson seal the three points for the U's making it two wins on the bounce, with their second home win this week.
The U's lined up at the JobServe Community Stadium with one change from their eleven that took three points against Forest Green Rovers in the week.
Ben Stevenson returned to the starters, with Luke Gambin dropping to the bench, and Marley Marshall Miranda dropping out of the matchday squad.
There were no early Colchester United goals in this game, with the visitors in fact having the best chances in the opening exchanges.
The ball was squared by Thomson to the centre with Tom Eastman making a good block as the visitors took aim at Gerken's goal.
Eastman had to be alert again when holding of Muldoon. A cross came in from the right flank again, with Eastman nodding away under pressure from the second top scorer in League Two.
And the U's were struggling to get a foothold in the game, with Harrogate enjoying much of the play.
Simon Weaver's side would be counting themselves unlukcy not to open the scoring on twenty-five minutes when, after Cohen Bramall's goal-line block. The U's left back initially gave the ball away in the area, forcing Gerken into a save from Aaron Martin, with the Harrogate forward's follow-up shot blocked and cleared by Bramall.
The visitors were forced in to a first half change, when Aaron Martin collided with the post after attacking a looping free kick. He was replaced by Jon Stead on thirty-seven minutes.
The U's kicked into life with time running out in the first half, with Chilvers and Pell both forcing saves out of Belshaw.
Match-winner against Forest Green, Noah Chilvers, chested the ball down and drove a low effort forcing a fine save out of the visiting 'keeper. And Pell saw Belshaw flying to his left to deny the U's captain as the whistle blew for half time.
The home side came out and started the second half as they ended the first, only this time they added the end product.
Callum Harriott struck his third goal of the season with a deflected finish over Belshaw in goal seven minutes in to the second period.
Ben Stevenson added to the tally two minutes later. After a flowing move with Poku and Welch-Hayes, Stevenson was there to finish off the move with a tidy controlled effort curled intot he far corner.
But the two-goal advantage was short lived. Harrogate were only a goal behind when Jon Stead, who came on in the first half for Martin, headed home from a corner with sixty-one minutes on the clock.
It gave the visitors confidence that they might go on and get an equaliser, piling the pressure on the U's goal for the remaining half hour.
But chances came and went for both sides, including the visitors striking the post, and going closest to getting level.
Brendan Kiernan's header struck the upright, with the U's at standstill before they were able to get the ball clear.
Steve Ball brought on Omar Sowunmi to sure up his defence, with the U's holding on for their second win at the JobServe Community Stadium in the week.
It's a result that lifts Colchester United up ninth in the league, with thirteen points, whilst Harrogate drop to sixth on fourteen.
Next up for the U's is a trip to the league leaders, at Newport, who have made their best ever start to a season in the EFL, after a 3-0 win at Bradford.
Colchester United starting XI: Gerken, Welch-Hayes, Bramall, Smith, Pell, Brown, Harriott, Chilvers, Eastman, Poku, Stevenson.
Subs: George, Sowunmi, Senior, Norris, Scarlett, Gambin, Bohui.
Harrogate Town starting XI: Belshaw, Fallowfield, Falkingham, Smith, Burrell, Thomson, Martin, Kerry, Muldoon, Miller, Hall.
Subs: Cracknell, Jones, Kiernan, Kirby, Stead, Walker.