During his spell with the Bluebirds, Bonner helped the club to three promotions in six seasons and suffered one relegation during the 1999–2000 season. The club reached the First Division in his time there, and he also played in their 2–1 victory over Premier League side Leeds United in the third round of the FA Cup in January 2002. In 2004, Bonner joined Oldham Athletic but suffered a career ending injury in September 2005 after breaking his arm in a match against Port Vale. After two surgeries on the arm, he was advised to stop playing by medical staff and subsequently retired from professional football in 2006 at the age of 32.