He continued his studies at the Basel Music Academy's Schola Cantorum Basiliensis from 1983 to 1987 under Jean-Claude Zehnder, Jesper Christensen and Jordi Savall, amongst others, and graduated in Early Music, Organ and Harpsichord. At this time he also began specializing in Italian music with Ferdinando Tagliavini.

In 1985 he was a prize-winner in the International Bach-Händel Competition of Bruges (Belgium) and in 1986 he received at Colmar in France the Regio-Förderpreis für Musik award instituted by the Academies of Basel, Strasbourg and Freiburg i.Br. For the publisher Gaus, he prepared the modern edition of previously unpublished works by Frescobaldi Fioretti and Claudio Merula Il primo libro dei Ricercari. Andrea Marcon won the first prize of the International Paul Hofhaimer Organ Competition in Innsbruck in 1986 and the first prize in the Harpsichord Competition of Bologna in 1991.

He has held master-classes and summer courses at Pistoia, Roskilde, Goteburg, Muri, Alkmaar, Nuremburg, Stade and Bielefeld, Les Andeleys, Daroca, and for the Music Academies of Toulouse, Hamburg, Copenhagen and Karlsruhe, as well as for the North German Organ Academy directed by Harald Vogel. He has been invited to take part in the jury of the International Pachelbel Competition of Nuremburg, the Schnitger Competition of Alkmaar/Amsterdam, and the Callido Competition of Borca di Cadore.

He founded in 1983 the Sonatori de la Gioiosa Marca, in 1989 the Organ Festival Città di Treviso e della Marca Trevigiana, in 1990 the European Academy of Castel Coldrano (Val Venosta), and in 1995 the Organ Academy Città di Treviso.

Highly active as a concert performer, he has played in the most prestigious festivals and musical centres of Europe - as organist, harpsichordist, and with the instrumental ensemble the Sonatori de la Gioiosa Marca &045 recording as well for various television and radio networks. His CD The heritage of Frescobaldi & Nacchini Organ, 1750 on Divox Antiqua) was awarded in 1996 with the renowned Preis der Deutschen Schallplattenkritik and The Antonio Vivaldi International Disc Award for Early Italian Music as the best artistic production of 1996 & Instrumental music sector. The following CD Sonatas for Organ by Domenico Scarlatti (Divox) won in 1997 as well the Preis der Deutschen Schallplattenkritik.

He teaches harpsichord and early Music Performance at the Schola Cantorum Basiliensis (Basle, Switzerland).