The House of Polyphony houses an ever growing collection of musical instruments to underpin its valorization projects. The instruments are tuned and maintained by young professional musicians. Whenever it is deemed necessary, service by specialized restorers or instrument makers is called upon.

Currently the collection consists of

• spinetta arpata, Jan Boon, Mechelen (BE), 2001, after an anonymous mid-sixteenth-century Italian model (Grassi Museum Leipzig nr. 41)
• harpsichord Jan Boon, Mechelen (BE), 2004, after Giuseppe Mondini ca.1700
• chamber organ, Hans ter Hart junior, Amsterdam (NL), ca.1840
• Italian organ, Carlo Russo, Naples? (IT), 1713
• gothic organ, Walter Chinaglia, Cermenate (IT), 2012, after a painting by Hugo Van der Goes, 1487
• harmonium, Christophe & Etienne, Paris (FR), s.d.
• Ottavino-spinet, Jan Boon, Mechelen (BE), 2006, after Franciscus Patavinus (Venice), 1527
• positive organ, Bert De Vylder, s.l., 1986
• Apfelregal, Christian Kögler, St. Florian (AT), 2021, built after an instrument from 1506
• positive organ, Hans Klais, Bonn (DE), 1957/58
• Clavichord, Joris Potvlieghe, Tollembeek (BE), 2002, after Phlipp Jacob Specken, (Stockholm?), 1743
• portative organ, Walter Chinaglia, Cermenate (IT), 2012 (long-term loan)
• portative organ, Noel Mander, London (UK), ca. 1985 (long-term loan)

Besides these keyboard instruments, a series of instruments are kept on long-term loan: fiddle, hurdy-gurdy, dulcimer, renaissance percussion instruments, flutes and bagpipes.