The U’s made two changes to their starting eleven for the game against the Iron, with Billy Clifford making his Colchester debut, and Alex Gilbey returning to the side after his short-lived appearance against Brentford.
A ninth defeat saw them drop below the Iron into the relegation zone for the first time this season.
Led by Freddie Sears, the U's chased down the game in the second half, but they couldn't find another goal to take something out of the match.
Once again, Joe Dunne's men put in a brave effort, but goals either side of half time left the U's with plenty to do.
The U's were left to rue crucial goals at important times of the game once again on Saturday, as Scunthorpe took the points in the crucial encounter at the bottom of League One.
In front of a vocal home support, the U’s went close within a couple of minutes as Massey was sent away on the right and fired over a low cross that Samuel got to but stabbed his shot wide of goal.
It was a vibrant start by the home side, with plenty of energy in the midfield as they looked to get the first goal of the game.
Rose pulled an effort past the near post after Clifford’s original shot was blocked, before Hawley saw a shot deflected over for a corner and Canavan was denied at the corner.
From that subsequent set piece, there was something of a melee in the U’s area, but the home side got bodies in the way to see of the danger.
It was a nervous moment for the home back line, but they stood strong, and Massey was proving a key influence in the game.
When Grella’s mazey run broke down and came to nothing, the U’s winger broke on the counter and flashed a shot wide of goal.
The visitors then had two great chances – albeit from a narrow angle – as first Ryan and then Barcham forced good stops out of Cousins.
Next, Wright weaved his way to the edge of the box for Clifford to have a shot deflected behind for a corner. The set piece was played low and captain Thompson’s shot was cleared off the line by Ryan.
The goal saver turned goal scorer four minutes before half time. Ryan picked up the ball thirty yards from goal and chopped back inside, firing in a thunderbolt into the top corner beyond the helpless Cousins.
The U’s made two changes at the break to try and get back into the game but they found themselves two down within 20 seconds of the restart.
The ball was played through to Hawley and he made no mistake as he tucked home past Cousins to double the Iron advantage.
It quelled the crowd at the start of the second period and it almost got worse as, from a free kick on the edge of the box, Kennedy smashed a shot off the top of the bar and away to safety.
The U’s fans found their voice, though, as their side fought to get back into the match, but watched on again as Hawley smacked another shot against the bar.
The home side fought their way back into the game with an hour gone. Sears took the initiative as he flew into the box. Morrison backheeled it to him and Sears smashed home a brilliant half volley to make it 1-2.
Thompson almost got an equaliser as his stabbed effort which looked destined for the bottom corner was deflected over the bar.
The U’s were well on top now as the momentum swung in their favour, with Sears instrumental in their attacking thrust.
They had half an hour to find a second goal, and Massey’s dart into the box with thirteen to go saw him shape a shot that went straight at Slocombe.
The visitors were doing their best to run the clock down and they did the job as they saw out the remainder of the game to get all three points.