He moved into management in November 1988 at Sheffield Wednesday, being promoted from assistant manager after Howard Wilkinson moved to Leeds United. Eustace was sacked after just three months and replaced by Ron Atkinson. He returned to football at Leyton Orient, working under Frank Clark, who moved from manager to managing director in 1991. Clark moved to Nottingham Forest in 1993, and Eustace was sacked a year later when the club failed to reach the play-offs.
Eustace returned to Sheffield Wednesday as a scout during Chris Turner's brief managerial tenure, but was made redundant as part of an overhaul of the coaching staff in 2006. His claim for unfair dismissal was rejected by an industrial tribunal.