After two seasons, Amoroso was soon on the move again, this time to Borussia Dortmund in Germany, for 50 million Deutsche Mark (€25 million), a German record at that time, and as of 2017, still a fifth highest signing after Corentin Tolisso, Javi Martínez, Mario Gómez, and Mario Götze. Amoroso won the Bundesliga title during the 2001–02 season, and was also the league's top scorer. He helped the club to the 2002 UEFA Cup Final, where his goal (a penalty) could not prevent the team from losing 3–2 to Feyenoord. During his next two seasons with the club, his appearances were more limited however, due to recurring injury problems. Amoroso played for Málaga during the 2004–05 season, although he was mainly used as a substitute, scoring only 5 goals in 29 appearances, as Málaga finished the season in 10th place in the league.