At the end of the 2007–08 season, Heaton agreed to move to Championship club Cardiff City on loan for the duration of the 2008–09 season. He was chosen as the club's first choice goalkeeper, above Peter Enckelman, for the start of the season by manager Dave Jones. He played in every match until late November, with the exception of the League Cup third round tie against Swansea City, when he was replaced by Enckelman. However, late on in Cardiff's 2–1 away defeat to Plymouth Argyle on 22 November 2008, Heaton picked up an injury and was forced off. The injury would go on to cost Heaton his place in the team as the club went unbeaten with Enckelman in goal for over two months.