Wilnis signed for Ipswich Town in January 1999. The Dutchman joined the Blues from De Graafschap for £200,000, replacing Mauricio Taricco. Wilnis quickly established himself in the side and was a key part of George Burley's side which won promotion to the Premiership. He made his debut for Ipswich in a 0–1 loss to Grimsby Town on 9 January 1999. Wilnis featured frequently during the remainder of the 1998–99 season as Ipswich finished 3rd in the First Division, losing out to Bolton Wanderers on aggregate over two legs in the First Division play-offs. He scored his first goal for the club on 3 April 1999, netting the final goal in a 6–0 win over Swindon Town.