Wise then captained Chelsea to victory over Real Madrid in the 1998 UEFA Super Cup, a late Gus Poyet strike securing a 1–0 victory in Monaco. His disciplinary issues were so severe during the 1998–99 season, that Wise missed no fewer than 15 matches in all competitions. He received three red cards in addition to being charged with biting the arm of Real Mallorca defender Elena Marcelino in the second half of their Cup Winners' Cup semi-final first-leg 1–1 draw at Stamford Bridge, though he was later cleared by UEFA. In the Premier League, he led Chelsea to their highest ever final position at the time, third, thereby securing a place in the Champions League for the first time in the club's history, losing only three leagues games along the way, a feat bettered by only three English champions in the 20th century.