Bayern Munich's 3–0 home win against Borussia Mönchengladbach on the open day of the 2005–06 season on 5 August. He first appeared in the 2005–06 Champions League in a 1–0 home win against Club Brugge on 27 September, where he was substituted onto the field for Paolo Guerrero in the 72nd minute. He would make just one more appearance in the competition, as Bayern Munich were eliminated by Milan at the round of 16. He scored his first goal of the season on matchday 8 in a 2–0 home win against VfL Wolfsburg on 1 October. In the following match, he scored after 19 minutes in a 1–1 away draw against Schalke 04 on 15 October. In Bayern's 4–0 win against MSV Duisburg one week later, on 22 October, he scored his side's third goal in the 59th minute. He encountered an injury which reduced him to just 13 Bundesliga appearances for the season. During this period of injury recovery, he spent some time with Bayern Munich II in the Regionalliga Süd. He returned to the first-team on matchday 29 in a 3–0 away loss to Werder Bremen on 8 April, where he was substituted onto the field for Claudio Pizarro in the 80th minute. Bayern claimed the 2005–06 DFB-Pokal when they defeated Eintracht Frankfurt 1–0 at the Olympic Stadium on 29 April, however Santa Cruz did not take part in the match. He scored his fourth and final goal of the 2005–06 season in a 3–1 home win against VfB Stuttgart on 3 May. During the 2006 DFL-Ligapokal, he featured in Bayern's 0–0 semi-final draw against Schalke 04 on 2 August, where he was substituted onto the field in the 77th minute for Lukas Podolski. Bayern eventually won the match 4–1 in a penalty shoot-out as he converted his side's third spot kick. Three days later, he played a full 90 minutes of the final where Bayern lost 2–0 against Werder Bremen on 5 August 2006. Bayern claimed the 2005–06 Bundesliga and qualified for the 2006–07 Champions League. Santa Cruz finished the season with three goals in 19 matches for the first team. He also made an appearance for the reserve team. 2006–07 season Santa Cruz made his first appearance in the 2006–07 Champions League in a 4–0 home win against Spartak Moscow on 12 September, where he scored Bayern's second goal with a right-footed shot in the 52nd