Wilnis scored a rare and memorable goal against Manchester United in the first home game after Ipswich's return to the top flight on 22 August 2000. He continued to be a key part of the Ipswich first-team throughout the season. On 20 November, he scored the winning goal as Ipswich won 1–0 away against Coventry City at Highfield Road. Ipswich defied expectations to finish 5th in the Premier League, earning a place in the UEFA Cup for the following season. Wilnis made 37 appearances during the season, scoring twice.