His fine form continued into the 2005–06 season which was Stelios' most successful as he was top scorer for Bolton with 12 goals, an impressive tally for a midfielder. One of the highlights of that season was the winning goal he scored against Arsenal in an FA Cup Fourth round match played at the Reebok Stadium on 28 January 2006. His form dipped slightly in the 2006–07 season where he missed several games through injury and failed to score any goals although he was still a regular player for the club with 28 games.