Badura-Skoda has performed a wide range of piano music and was a close friend to Swiss composer Frank Martin, who dedicated his Piano Concerto No. 2 to Badura-Skoda, in addition to some smaller works. But Badura-Skoda's name is most closely related to the Viennese classicists, Mozart, Beethoven, and Schubert, whose keyboard works, including whole cycles of sonatas, he has recorded, in some cases multiple times. Beginning in the 1950s, Badura-Skoda began to quietly make the case for the use of late eighteenth and early nineteenth century keyboards in the interpretation of this literature, anticipating the period instrument boom by decades. In this respect, Badura-Skoda was helped and to some degree influenced by the work of his wife, musicologist Eva Badura-Skoda. Paul Badura-Skoda has also played in a four-hand piano duet with fellow countryman Jörg Demus, and the pair collaborated on a book, Die Klaviersonaten von Ludwig van Beethoven, which was published in 1970.
Badura-Skoda's recording career encompasses an enormous number of recordings. He began with a justly famous series of discs on the Westminster label in the early 1950s and since then has recorded for Deutsche Grammophon, Astreé, Arcana, Music & Arts, Sanctuary Classics, Jecklin-Disc, Harmonia Mundi, and many others. In 2003 Badura-Skoda embarked on a world tour to celebrate the occasion of his 75th birthday. Badura-Skoda also composes; among his works are a Mass in D.