During the 2003–04 season, Bonner made 20 appearances for the Bluebirds but fell out of favour at the club, making his final appearance in December 2003 as injuries decreased his playing time. He grew unhappy after he and teammate Gareth Whalley were excluded from the side due to a potential contractual bonus being triggered if either of the pair played another league fixture for the club. He left the club in March 2004 after being released. Prior to his release he commented, "It's disappointing to go, but things have gone a bit stale and it's time to move on for the good of my football future."