After the 1996 FA Cup Final, Jones was advised to take a six-month break from football due to back problems. He returned to action, but the next two seasons were plagued by injuries, and in April 1998 he played what was to be his last game for Liverpool against Chelsea. An injury in his left knee could not be fixed, despite three operations, and at the end of the 1998–99 season, in which he had not played a game, he was released on a free transfer by new coach that year, Gerard Houllier, who was ushering in a new era at the club to eliminate the club's Spice Boys public image and stereotype.