The U’s chairman is hoping that Tony Humes’ appointment as first-team manager will see the club move away from their current position in the relegation zone.
But Cowling admits that they are currently punching above their weight in the third tier, pitting their wits against teams with bigger budgets and support.
Cowling has ploughed considerable funds into the club’s academy and Florence Park training ground, in Tiptree.
But he has steadily been cutting the playing budget by £300,000 every year and plans to reduce his subsidy to zero by 2016, in a bid to make the club more sustainable and in line with Fair Play rules.
And while he feels Colchester’s long-term future is bright, the U’s supremo concedes that it will take time for the full rewards of the youth system to bear fruit.
Cowling said: “We’re a club that is punching above our weight in many, many ways.
“We may have a nicer stadium than some and a nice training ground.
“But what goes out on the pitch is really dictated by the budget - and that’s dictated by how many fans turn up and watch us.
“You can see where we are and every year, we maintain our status.
“At this moment, we’re doing well and hopefully in a few years as we see more of this talent come through, we can perhaps do better regardless of how many people come and watch us but that’s going to take some time.
“We’re seeing some of the benefits already of what we’ve done.
“But we’re going to have a couple more tough years and I’ve never said anything other than that, since we had to rip the heart out of the playing budget.
“Some people might feel that the club went backwards under Joe (Dunne).
“But they don’t understand what’s going on in the background of football, what’s been forced upon us and how that could impact the club.”
Cowling stressed that he has appointed Humes as the club’s new first-team manager for the long term.
The U’s chairman has declined to reveal the length of Humes’ contract but says he will give the former Ipswich Town defender his full backing.
“Colchester doesn’t have as big a turnaround of managers as maybe some other clubs,” added Cowling.
“We’re not trying to join this merry-go-round that everybody else has had.
“We’re appointing someone who we expect to be at the club for quite some time.
“Tony, like the rest of the managers, will get my full backing to achieve what we want to achieve.”
For four pages of Colchester United coverage, including the views of Cowling, Humes, Richard Hall and Paul Abrahams, see Wednesday's Daily Gazette.