The start of the 2008–09 season saw Capaldi sidelined due to a knee problem. After sitting out the first fortnight of the season, he returned to first-team action on 26 August in a 2–1 League Cup victory over Milton Keynes Dons, only for him to suffer a recurrence of the problem. Capaldi spent over three months on the sidelines with the injury and, after being named on the bench for several games, made his return as a substitute for Chris Burke during a 0–0 draw with Arsenal in the fourth round of the FA Cup on 25 January. He featured in just five matches for the club throughout the season.