Despite starting the first few games relatively brightly for Colchester United under then manager Paul Lambert, Beevers sustained an injury to his shoulder during a competitive match against Milton Keynes Dons. This resulted in him missing three months of the season, over which period he was plagued by other smaller injuries postponing his return to action. Due to his long absence and lack of fitness, he failed to make an impact in the 2009–10 season and didn't manage to break back into the starting line-up, only making a handful of substitution appearances.