On 27 September 2013, McNaughton joined Bolton on a 28-day emergency loan deal. He made his first appearance for Wanderers four days later in a goalless draw with local rivals Blackpool at Bloomfield Road. After becoming the club's first choice right-back during his stay with Bolton, he scored his first goal for the club in the 1–1 draw with Charlton Athletic on 21 December 2013, this was his first goal in the League since scoring for Cardiff against Barnsley in May 2008.