Lee Barnard struck the woodwork in an otherwise uneventful first half but Sky Blues took a grip of the game with two quick goals after the break.
Christian Ziege pulled a goal back with a trademark free-kick but the home side finished the stronger and clinched it with a third in the last minute.
It was only the third defeat in our last 16 FA Premier Reserve League fixtures but nevertheless, coach Clive was down afterwards.
"We wanted to go out with a win and a performance in the last game and we didn't get that," said Clive.
"We let the game slip in the second half after not taking chances in the first half and I made the point to the lads that it doesn't matter whether it's first team, reserves or lower levels, if we're not going to do it right we'll get punished.
"It's about winning habits. You have to have a strong mentality. We came up against a young, enthusiastic side again and you have match these teams before our ability comes through.
"I've absolutely no doubt there is a lot of talent in that dressing room but it's about how you use that ability and we didn't do that on this occasion."
Clive Allen couldn't hide his disappointment as our reserves ended what had been a positive end to the season on a low note at Coventry City last night.