Before even playing a Bundesliga match, Lizarazu lifted a trophy with his new club, winning the inaugural edition of the preseason DFL-Ligapokal. It was the start of a highly successful spell in Bavaria, despite the interruption of some serious injuries, as he went on to win six Bundesliga championships (including three in a row between 1999 and 2001), as well as five DFB-Pokals, the Champions League in 2001 (scoring his penalty in the shootout), and the Intercontinental Cup. On winning the Intercontinental Cup in 2001, he became the first player to be a current European and World champion in both club and international football.