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 is 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he founded the ensemble La Gioia Armonica, which produced under his direction world-premiere recordings of hitherto unpublished works by Antonio Caldara, Johann Georg Reutter, Giambattista Martini and Antonio Sacchini, in collaboration with the lables cpo, Ramée and with Radio Bremen.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 or the Mitteldeutsche Heinrich-Schütz-Tage.
In 2017 and 2018 Jürgen Banholzer taught solo singing and vocal chamber music at the International Summer School of Early Music in Valtice (Czech Republic).
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, as well as with notable period orchestras and ensembles such as Concerto Köln, Il Seminario Musicale, Das Kleine Konzert, Concerto poetico Zürich, L’arpa festante, L’Orfeo, La Gamba. His recording of solo cantatas by Antonio Caldara was released to great acclaim. He appeared in opera productions at the Ludwigsburger Festspiele, the Festival de Musique du Haut-Jura, the Wiener Festwochen, the Bayerische Staatsoper / Prinzregententheater, the Feldkirch-Festival and in the Festspielhaus Baden-Baden. As an ensemble singer he worked with groups such as the Huelgas Ensemble, the Johann Rosenmüller Ensemble, Capella Ducale & Musica Fiata, the Clemencic Consort, La Fenice, Weser-Renaissance, La Chapelle Rhenane, Balthasar-Neumann-Chor, and the Amsterdam Baroque Choir at festivals throughout Europe and in the USA and China.
From 2004 to 2014 Jürgen Banholzer taught figured bass, musical analysis and historical techniques of composition at the Musicology Department of Mainz University.