Following two more seasons as the Avalanche backup, Aebischer became Colorado's starting goaltender following Roy's retirement in the summer of 2003. He played 62 games and posted 32 wins during the 2003–04 season. That season, he started his first career playoff game for the Avalanche and led Colorado to the second round, where they lost to the San Jose Sharks in six games. The following season, due to the NHL lockout, Aebischer returned to Switzerland and played for HC Lugano in the Nationalliga A.