During his time at Ninian Park, Bonner played key roles in avoiding relegation back to the Third Division and the eventual promotion to the First Division, helping the club to three promotions during his six-season stay and suffering one relegation during the 1999–2000 season. He also played in the 2003 Football League Second Division play-off Final at the Millennium Stadium as a late substitute in place of Andy Legg as Cardiff defeated Queens Park Rangers 1–0 to win promotion. He was also part of the side that caused a FA Cup upset by defeating Premier League leaders Leeds United in the third round during the 2001–02 season.