Poyet joined Chelsea on a free transfer in June 1997. Not long into his first season at the London club, he suffered cruciate ligament damage, this meant he missed the victorious 1998 Football League Cup Final but recovered to play in the team's successful Cup Winners' Cup Final against VfB Stuttgart. The following year, he contributed 14 goals – making him the club's second highest scorer – to help Chelsea finish third in the Premiership, including a crucial headed goal in 1–0 win against Leeds United. He also scored the winner for Chelsea in the 1998 UEFA Super Cup against Real Madrid. In 1999–2000, he scored 18 goals (which again made him Chelsea's second highest scorer), with a scissors-kick volley against Sunderland, a long range strike against Lazio, and both of Chelsea's goals in the FA Cup semi-final against Newcastle United, among the most memorable, as the team won the FA Cup and reached the UEFA Champions League quarter-finals.