Morientes performed very well in the 1998–99 campaign, scoring 19 goals in the league and 25 in 38 appearances overall. He continued to display top football in 1999–2000, netting 19 times and finishing as Real's top scorer in a year where he also helped to the capital side's second Champions League title in three years, scoring in the 3–0 defeat of Valencia CF in an all-Spanish final. In the next season, he won the first of two league titles with the club and netted ten goals overall, including four in eight appearances in the Champions League in a semi-final exit to eventual winners FC Bayern Munich – he missed the last weeks due to injury.