Born in Unter Sankt Veit, today Vienna, Mottl was regarded as one of the most brilliant conductors of his day. He composed some operas, of which Agnes Bernauer (Weimar, 1880) was the most successful, and numerous songs and other music. He was also a teacher, counting among his pupils Ernest van Dyck.
Mottl had a successful career at the Vienna Conservatoire. He became known as a gifted conductor of Wagner's music, and assisted Hans Richter in the preparations for the first complete Ring Cycle at Bayreuth; in 1886 he directed the performance of Tristan und Isolde at the Bayreuth Festival. From 1881 to 1903 he was conductor at the Karlsruhe Opera, and made a wide reputation for his activity there, particularly in producing the works of Wagner and Hector Berlioz. In later years, as a conductor of Wagner especially, he visited London and New York, where he was guest conductor for the Metropolitan Opera in 1903. In 1904 he was made a director of the Akademie der Künste at Berlin.
In June 1907 he cut some player piano rolls with Welte-Mignon, including his own piano transcription of the Prelude, the Love Duet and Brangäne's Warning from Tristan. He died in a Munich hospital on July 2, 1911, after suffering a heart attack on June 21, while conducting his 100th performance of Tristan in Munich.