He made his first appearance of the season on the opening day, featuring as a second-half substitute in a 3–1 home win over Nottingham Forest at Portman Road.

Wilnis started the first leg of the play-off semi-finals away at the University of Bolton Stadium, with the match ending in a 2–2 draw after Ipswich came back from 0–2 down following a brace from Marcus Stewart.

[6] 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.

Ipswich defied expectations to finish 5th in the Premier League, earning a place in the UEFA Cup for the following season.

[7] After Chris Makin's recruitment in 2001, Wilnis played fewer games and looked to be on his way out of the club after falling out with manager George Burley after being substituted in the first half of the UEFA Cup tie at Helsingborg late in 2001.

He saw his game time reduced during the 2001–02 season, making 19 appearances in all competitions as Ipswich suffered relegation from the Premier League following an 18th-placed finish.

He was a regular during the season, mainly at right-back whilst also often playing at left-back and latterly at centre-half during the former England striker's tenure as manager.

He continued to keep his place as the starting right-back in the team, making 46 appearances in all competitions and helping Ipswich reach the play-offs in the 2003–04 season by finishing 5th in the First Division.

[11] In Wilnis' 2009 autobiography, he wrote: "I got letters saying I was a dead man and threatening to break my arms and legs if I ever set foot in Norwich.

He helped the team reach the Championship play-offs once again as Ipswich finished 3rd in the league, narrowly missing out on an automatic promotion place.

The revival of form by Spanish defender Sito Castro and the strong partnership of Alex Bruce and Jason de Vos, made it hard for Wilnis to break back into the side.

A stunning own goal from Colchester defender Magnus Okuonghae and a strike from Jordan Rhodes gave the Blues a 2–0 victory.

Fabian Wilnis made his final appearance in a Town shirt with 12 minutes left, his every touch applauded by the Blues supporters.