After his habilitation with the topic Zur Entwicklungsgeschichte des Wiener klassischen Still (On the Developmental History of Viennese Classical Style) in 1915, he was appointed professor in 1923.
In 1928 he took over the chair of musicology at the University of Innsbruck as successor of Rudolf von Ficker.
When a "Gauverbot" was imposed on him for Tyrol in 1939, he had to move back to Vienna and was employed in a metal factory as a forced labourer until 1945.
Other family members were murdered in The Holocaust, including his sister in the Auschwitz concentration camp.
In 1945 Fischer was rehabilitated and appointed director of the Music and Arts University of the City of Vienna until 1948.