On 7 July 2008, Marc Wilson signed a new three-year contract at Portsmouth. He made his Pompey debut coming on as a substitute for Richard Hughes in a 4–0 League Cup 3rd round loss to Chelsea on 24 September 2008. Wilson excelled playing at right-back on his first start for Portsmouth in a 3–0 UEFA Cup victory over Heerenveen. On Boxing Day 2008, Wilson started his first Premier League match in the 4–1 loss at home to West Ham. On 5 August 2009, it was revealed that Wilson had been involved in an alleged bust-up with fellow team-mate David Nugent during Portsmouth's pre-season trip to Portugal. Both players were sent home and consequently fined two weeks wages by the club.