Paddy Madden hit a brace for United, and Tom Hopper made the perfect return to first team action by finding the back of the net too.
The Iron made three changes going into the game, with Scott Wiseman, Conor Townsend and Hopper coming in for Jordan Clarke, Scott Laird and Kevin van Veen respectively.
Elsewhere, Luke Daniels started in goal, there was a back four of Wiseman, David Mirfin, Murray Wallace and Townsend. In midfield, there was a trio of Neal Bishop, Stephen Dawson and Jamie Ness, and in attack Madden and Luke Williams provided support to the returning Hopper.
The Iron were quick out of the blocks, and almost had a golden opportunity inside the opening minutes, when Williams picked the ball up and drove for goal. However, the attacker was cynically brought down just outside the area. Williams took the resulting free-kick himself, but it was well defended by the visitors.
After a positive start to the match from United, it was in fact the visitors who were the first to have an effort on goal. But, despite stealing a yard at the near post, U's forward Chris Porter could only direct his header wide of Daniels' goal.
Kevin Keen's side were posing a threat on the break, and they gave the Iron defence something to think about again, twenty minutes in, when Marvin Sordell curled an effort towards goal. But the former Watford man got too much elevation on the strike, and he could only watch the ball sail over the crossbar.
Winger George Moncur was the next to try his luck, but much like his team-mate Sordell, he did little to worry Daniels, as he fired harmlessly over.
As the opening period wore on, the threat from the away side gradually deteriorated, and United were able to get more of a foothold in the game. Five minutes before the break, Dawson sent a looping effort towards goal, but he was denied by a goal-line clearance from Richard Brindley.
Moments before the interval though, the Iron had to survive another scare when Alex Gilbey burst into the box. It took some heroic last ditch defending from Wallace to prevent the midfielder from testing Daniels.
This would turn out to be the last action of the half, as the two sides went in level at the break.
United's start to the second period was a good one, with Townsend rising highest at the back post, to head Madden's cross goalwards. But in spite of his good leap, the full-back could only head into the arms of Jake Kean.
The best opening in the game to that point came shortly after, when Dawson got onto the end of a Madden flick on, and it looked as though the net would bulge when the skipper struck for goal. But the Irishman had to painfully watch his effort strike the outside of the post.
Fifteen minutes into the half however, the visitors' resistance was broken. Mirfin, who'd stayed up from a set-piece, slipped a fantastically weighted pass into Townsend, who then picked out Hopper at the near post, and the returning frontman finished neatly over Kean.
Two minutes later, Hopper went from goalscorer to provider. The forward turned well in the box, and then had the awareness to poke the ball through to Madden, who finished off the underside of the crossbar.
United were threatening to run riot, and shortly after doubling the lead, the advantage became three. Madden once again was the goalscorer and yet again he finished well, after turning his man and firing low into the bottom left corner.
Kyle Wootton was introduced with around twenty minutes to go, and the striker nearly got in on the goalscoring act too. He firstly linked well with Madden, before firing a volley at U's 'keeper Kean from close range.
With a bit more care and composure in the final third, the Iron could have added even more gloss to the scoreline. But they'd have to settle for three, in a match which the visitors were blown away by a ruthless second half display from United.
Scunthorpe United: Daniels, Wiseman, Mirfin, Wallace, Townsend, Bishop, Dawson, Ness (King 79), Madden, Hopper (Wootton 73), Williams (Adelakun 88).
Substitutes not used: Anyon, Laird, Clarke, Henderson.
Colchester United: Kean, Garvan, Briggs, Wynter, Gilbey, Porter, Moncur (Massey 69), Eastman, Brindley, Edwards (Ambrose 68), Sordell (Bonne 77).
Substitutes not used: Elokobi, Wright, Shorey, Parish.