Santa Cruz debuted for Bayern Munich in the 1999–00 Bundesliga season in a 2–0 loss against Bayer Leverkusen on 22 August 1999.
Six days later, he scored his first league goal in the 40th minute of a 1–0 win against SpVgg Unterhaching on 28 August.
He made his first appearance in the 1999–2000 UEFA Champions League on 15 September in a 2–1 victory over PSV.
His first goal in the Champions League came on his fifth appearance in the competition as Bayern lost 2–1 against PSV, as was substituted onto the field on 26 minutes for Paulo Sérgio and scored with a right-footed shot on 51 minutes.
He ended the season with five goals in 28 league appearances as Bayern were crowned champions of the 1999–2000 Bundesliga season.
Santa Cruz had also made consecutive Champions League appearances until the semi-final stages where Bayern Munich were knocked out by Real Madrid.
On 6 May 2000, he was substituted onto the field on 73 minutes for Carsten Jancker during the 1999–2000 DFB-Pokal final as Bayern Munich beat Werder Bremen 3–0.
Santa Cruz finished the season with nine goals in 48 matches.
Santa Cruz debuted for Bayern Munich in the 1999–00 Bundesliga season in a 2–0 loss against Bayer Leverkusen on 22 August 1999. Six days later, he scored his first league goal in the 40th minute of a 1–0 win against SpVgg Unterhaching on 28 August. He made his first appearance in the 1999–2000 UEFA Champions League on 15 September in a 2–1 victory over PSV. His first goal in the Champions League came on his fifth appearance in the competition as Bayern lost 2–1 against PSV, as was substituted onto the field on 26 minutes for Paulo Sérgio and scored with a right-footed shot on 51 minutes. He ended the season with five goals in 28 league appearances as Bayern were crowned champions of the 1999–2000 Bundesliga season. Santa Cruz had also made consecutive Champions League appearances until the semi-final stages where Bayern Munich were knocked out by Real Madrid. On 6 May 2000, he was substituted onto the field on 73 minutes for Carsten Jancker during the 1999–2000 DFB-Pokal final as Bayern Munich beat Werder Bremen 3–0. Santa Cruz finished the season with nine goals in 48 matches.
Roque Santa Cruz