Jürgen Banholzer studied the organ in Boston (USA) with James David Christie, at the Musikhochschule in Stuttgart with Ludger Lohmann (on a scholarship from the Studienstiftung des Deutschen Volkes) and with Jean Boyer at the Conservatoire National Supérieur de Musique in Lyon. He went on to study singing at the Schola Cantorum in Basle and was later awarded a PhD in musicology at the University of Mainz.
As an organist he has given recitals in Germany, Austria, France and Switzerland. His main interest lies in organ music and organs of the 17th and 18th centuries. As a continuo player on harpsichord and organ he has been a guest in groups like the Johann Rosenmüller Ensemble, Freiburger Barockorchester, Balthasar-Neumann-Ensemble, L'Arpa festante, La Dolcezza or Stefan Temmingh & Ensemble.
Together with the Austrian dulcimer player Margit Übellacker he founded the ensemble La Gioia Armonica, which produced under his direction world-premiere recordings of hitherto unpublished works by Antonio Caldara, Johann Georg Reutter, Giambattista Martini and Antonio Sacchini, in collaboration with the lables cpo, Ramée and with Radio Bremen. The critics commented on these CDs: „a delightful range of charming colours and intriguing textural effects“ (Early Music); „brilliant interpretation“ (Goldberg); „breathtakinkly lovely“ (BBC Music Magazine). The ensemble has since been invited to festivals like the Händelfestspiele Halle, Ton Koopman's Itinérarie Baroque, the Dordrecht Bachfestival, the Timisoara Early Music Festival, Bagnacavallo Classica or the Mitteldeutsche Heinrich-Schütz-Tage.
Since 2017 Jürgen Banholzer has taught singing and vocal chamber music at the International Summer School of Early Music in Valtice (Czech Republic). He has taught at the Mainz Conservatory and at the Musicology Department of Mainz University.
Until 2010 Jürgen Banholzer performed as a countertenor soloist in concerts, radio broadcasts and CD recordings under conductors such as Thomas Hengelbrock, Ivor Bolton, Harry Christophers and Jean-Claude Malgoire. His recording of solo cantatas by Antonio Caldara was released to great acclaim. As an ensemble singer he worked with groups such as the Huelgas Ensemble, the Johann Rosenmüller Ensemble, Balthasar-Neumann-Chor, and the Amsterdam Baroque Choir.