On 4 December 2001, he opened the scoring with a curling free kick against Deportivo de La Coruña in the 64th minute, as Bayer comprehensively beat the Spanish side 3–0 in the second group stage of the Champions League. Following Bayer's victory over Liverpool in the quarter-finals of the Champions League on 9 April 2002, Zé Roberto announced that he would be joining former teammate Michael Ballack at Bayern Munich. Despite the transfer distractions, Zé Roberto helped Bayer reach the final of the Champions League on 15 May 2002, losing 2–1 to former club Real Madrid in Glasgow. In four years at the club, Zé Roberto appeared in 113 league matches scoring 16 goals.