In 2009–10 Wilson became a first choice player in the Pompey side that was relegated and reached the FA Cup final although Wilson himself did not play in the final due to injury. Though his performances as a central defender earned him criticism, he impressed after returning to his natural position of centre midfield towards the end of the season. On 5 February 2010 Wilson signed a new three and a half-year contract to stay at Portsmouth to the end of the 2012–13 season. After Portsmouth's relegation to the Championship Wilson was handed the number 6 shirt after previously wearing 35 and was named as captain. At 22 years old he became one of the youngest permanent captains in the club's history. However manager Steve Cotterill revealed that Wilson was close to a transfer to Premier League side Stoke City.