But the U’s chairman admits he is braced for another testing campaign next season, in the wake of further budget cuts.
Cowling has worked with Geraint Williams, Paul Lambert, Aidy Boothroyd and John Ward during his seven-year spell at the U’s helm.
But he regards current Colchester boss Dunne as the hardest-working of those managers.
And ahead of the club’s glitzy awards dinner at the Weston Homes Community Stadium tonight, Cowling feels a well-earned rest for the Irishman is long overdue.
“I’m absolutely delighted for Joe,” said Cowling, who saw Colchester secure a 16th-place league finish this season.
“He’s the hardest-working manager I’ve ever worked with and it’s been the same again, this year.
“I want Joe to now take a good couple of weeks off, where he doesn’t think about it at all.
“I know that he doesn’t find it easy fighting a relegation battle with Colchester.
“But at the moment, that’s where we are and I’m sure it would be the same with any other manager."
For more on this story and all of the other latest Colchester United news, see Friday's Daily Gazette.