During a pre-season friendly against Celtic on 22 July 2009 he suffered an ankle injury which kept him out for the opening two months of the season. After appearing for the club's reserve side, he returned to the first team on 17 October 2009 as an unused substitute during a 1–1 draw with Crystal Palace but suffered a recurrence of the injury kept him out until 17 November 2009 when he played 45 minutes of a reserve team game against Hereford United. He returned to the line-up on 21 November 2009 against Barnsley, but was taken off in the 21st minute for Paul Quinn with a back injury. On 23 November McNaughton was sent to have a scan on the back injury, which the club's medical staff believed to have caused the problem and resulted in him being out for two weeks. On 5 December 2009 McNaughton played his first 90 minutes of the season in a 1–0 win over Preston North End. The next season his injury worries ceded and he has played in every league up to and including the game against Barnsley. McNaughton was Cardiff's most consistent defender throughout the 2010–11 season, and won the Player of the Year award.