He conducted the Wiener Tonkünstler Orchestra from 1914 to 1917, and became head of the Mozarteum Salzburg in 1917. There, he played a major role in the founding of the festival and has also conducted serenade concerts.
As a composer, Bernhard Paumgartner composed operas, cantatas, songs and choirs. His songs and instrumental chamber music are still played occasionally. In 1922 he published The Taghorn, a collection of works of minstrels. As an author he was known for his biographies about Mozart and Bach. His autobiographical memories also attracted attention.
After the Anschluss of Austria, Paumgartner was relieved of his duties as director of the Mozarteum by the National Socialists. Paumgartner spent the war years on a research assignment at the University of Vienna, and later in Florence. From 1952, Paumgartner was the founder and director of the Camerata Academica of the Mozarteum Salzburg. He was co-founder of the Association Européenne of the Conservatoire, Académies de Musique et Musikhochschulen. In 1955, he was musical director of the film adaptation of Mozart's Don Juan - Opernfilm (directed by Walter Kolm-Veltée) with the Wiener Symphoniker and a large ballet. From 1960 to 1971 he was President of the Governing Board of the Salzburg Festival.