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The U’s midfielder heads back to former club Northampton Town this lunchtime fresh from scoring a dramatic late equaliser at Chesterfield in midweek.
Perry, who has fought his way back from a long-term knee injury, impressed during a previous loan spell at Sixfields.
But Cowley insists Colchester must not rush him back.
“Saturday, we have to be careful with him, because we just want to play him but we do have to keep building,” said the U’s boss.
“He obviously goes back to a ground that he’s familiar with, in Northampton.
“It was his first loan and he did really well there under Kevin Nolan, in League One.
“He played a big part in keeping them in the division.
“It was a great moment for him. We all know how hard it’s been for him, behind the scenes.
Great moment - Ben Perry celebrates after scoring Colchester United's late equaliser at Chesterfield (Image: Richard Blaxall)
“It will give him a big shot of momentum and maybe confidence and belief as well, which he should have had anyway, because he’s a really competent boy.”
Perry spent time on loan at Northampton from Nottingham Forest in the 2024/25 season, making 17 league and cup appearances for the Cobblers.
“I really enjoyed my time there," said Perry.
“I was only there for a couple of months but it was my first stint in men’s football.
“Hopefully, I can go back there on Saturday and get a win!"
Perry’s return boosts an injury-hit U’s squad that will again be without Jack Payne, Harry Anderson and Kylian Kouassi at Northampton.
Colchester’s injury troubles began on the opening day, when Teddy Bishop went off after two minutes and his replacement, Jake Leake, dislocated his shoulder before half-time.
Cowley said: “Looking back at the first game, we should have known what was to come and sometimes, they come in droves.
“We’re just working hard with the players that we’ve got and the boys that are not playing are all really good professionals, doing all they can to get fit.”
Lunchtime mission - Colchester United head coach Danny Cowley takes his side to Northampton Town today (Image: Richard Blaxall)
Colchester must also contend with an early start at Sixfields at the end of a three-game week.
“Away from home, I think a lunchtime kick-off does make some difference, particularly in a three-game week,” Cowley added.
“But it’s nothing that we can’t handle.”