The U's cup exploits eventually led to a late season drop in form, as they slipped from 5th position to 14th with fixture congestion.

Helped by the astute signings of Wayne Andrews and Premier League youngsters Craig Fagan and Rowan Vine, Colchester reached the FA Cup fifth round, defeating Oxford United, Aldershot Town, Accrington Stanley, and Coventry City, courtesy of a Vine hat-trick, before succumbing to Sheffield United 1–0 at Bramall Lane.

Two days after the FA Cup clash, the U's were faced with the task of overcoming a Football League Trophy southern section final first-leg 3–2 deficit against Southend United.

Fixture congestion was a contributing factor in Colchester's slip down the table from 5th position to 14th, while losing Karl Duguid to a serious knee injury.

At the end of the season, Colchester completed the campaign in eleventh position, nine points adrift of the play-off places.