Asperen's repertoire on harpsichord, organ, and clavichord is expansive and ranges from the music of John Bull to that of Antonio Soler, whose works Asperen has recorded in their entirety. Asperen has also recorded the complete published keyboard output of Carl Philipp Emanuel Bach and Jan Pieterszoon Sweelinck. Among the record labels that Asperen has recorded for are EMI, Sony, Virgin, Teldec, Deutsche Harmonia Mundi, N.M. Classics, and Astreé; his recordings have won many awards, including the Deutsche Schallplattenpreis. As a musicologist, Asperen has prepared many editions and reconstructions of works by composers from the Low Countries, particularly on behalf of Dutch Baroque composer Cornelis Thymanszoon Padbrué, but also members of the van Noordt family and naturally, Sweelinck
. Asperen has also rehabilitated a few works of Johann Sebastian Bach that were not previously known; he has recorded the multiple keyboard concerti of Bach with his former professor Gustav Leonhardt
. Since 1999, Asperen has been recording with the Aeolus label, using historic instruments to perform the music of Bach, Louis Couperin, and Froberger.