Manager Ian Atkins left for a coaching role at Birmingham City in the summer after narrowly missing out on the Conference title the previous campaign.

In the FA Cup, Colchester went out in the first round to Exeter City, while McDonough fielded a weakened side in the Bob Lord Trophy, crashing out 6–2 to league rivals Wycombe.

However, in the FA Trophy, following two replay wins in the first two rounds of the competition, the U's reached the Wembley final, where they faced Witton Albion, who had dumped them out at the quarter-final stage the previous season.

Following Ian Atkins decision to return to Birmingham City in a coaching capacity, new chairman James Bowdidge appointed Roy McDonough in a player-manager role.

His long upfield goal kick in the 90th minute of the game bounced over Wycombe goalkeeper Paul Hyde and sealed what would prove to be a vital 2–1 win.

As 1992 dawned, Colchester found themselves seven points ahead of nearest rivals Wycombe in the league, but 16 home wins in succession failed to shake off their Buckinghamshire counterparts.