Skuse spent the first three months of the 2005–06 season in the team of new manager Gary Johnson, but was in and out of the team the rest of the season. He signed a new deal in January 2006, this time a four-year contract keeping him tied to the club until the summer of 2009. Skuse scored his first goal for his club, a penalty in the 6–0 win over Gillingham on 18 March 2006. His first goal from open play came the following week away to Rotherham. Skuse finished the season having made 29 starts in the league, as the club finished in 9th position, six points shy of the promotion play-offs.