Ipswich had been relegated 18 months before Wark's return to the club and were still playing in the second tier of English football. During this second spell at Ipswich, Wark was close to being an ever-present in the side: he missed just two games in two seasons. He was the club's equal top-scorer in the 1988–89 season, sharing the achievement with forwards Dalian Atkinson and Jason Dozzell.
Following three seasons of mid-table finishes,[nb 3] manager John Duncan was sacked and replaced by John Lyall. With his contract expiring, Wark received what he considered to be a "derisory" offer from Lyall, which he declined. Once he became a free agent, Wark signed on a free transfer for Second Division rivals Middlesbrough in August 1990. In his two additional seasons with Ipswich, Wark had scored 20 goals, and won the club's Player of the Year award in both seasons.