After seven years and four managers in his time at Bloomfield Road, Bonner moved south to join Cardiff City in 1998 on a free transfer after turning down a new contract at Blackpool, stating "I felt I was going a bit stale and I needed a new challenge. It was nothing to do with Blackpool or the people connected with the club, I just felt it was time to move on." Another reason Bonner chose Cardiff was the presence of his former Blackpool manager Billy Ayre at Ninian Park, describing him as "almost like a second dad to me", where he was assistant manager to Frank Burrows. Ayre would later replace Burrows as manager during the 1999–2000 season as the club struggled. He soon established himself in the side but after suffering from injury he was unable to reclaim his place and was allowed to join Third Division side Hull City on a one-month loan deal, alongside Blackpool midfielder Gary Brabin. In debut for the club, he scored the winning goal against Rotherham United, but the loan spell was cut short when he suffered an ankle injury in training and was sent back to Cardiff, with the Rotherham game being his only appearance for the club.