Niels Pfeffer studied basso continuo, harpsichord, guitar, and lute in Stuttgart, Freiburg, The Hague, and Basel. He feels at home with almost everything that is plucked or has keys. Influential teachers for him included Johannes Monno, Jörg Halubek, Robert Hill, Zoran Dukic, Jörg-Andreas Bötticher, and Julian Behr.

He teaches the theorbo at the Stuttgart University of Music and accompanies on the harpsichord and lute. He also has an assignment for accompaniment on these instruments at the Schola Cantorum Basiliensis. In addition, he works as an academic staff member at the University of Tübingen, where he teaches on topics of historical performance practice and is pursuing his own dissertation project on piano roll recordings from the early 20th century.

With his instruments, he has played with numerous orchestras and festivals, including the Nordic Baroque Orchestra, Rotterdam Philharmonic Orchestra, Capricornus Consort Basel, La Cetra, and the Bach Foundation St. Gallen. With the ensemble "La Visione", he recorded all of Georg Philipp Telemann's "Essercizii Musici" on 4 CDs. In 2019, he won third place at the first international competition for Continuo and Partimento in Katowice.

Niels Pfeffer has made television and radio recordings, concerts, and masterclasses in countries such as Estonia, Lebanon, Armenia, and Mexico. During his studies, he was supported by a Germany Scholarship and an Excellence Scholarship from the Royal Conservatory of The Hague.