ABSTRACT This paper investigates the role played by Italian naturalist, Filippo Buonanni (1638–1723), in the reorganization of the Kircher Museum. Specifically, it considers Buonanni’s unique philosophy of nature, which can be gleaned from his public debates about spontaneous generation and fossil formation. This paper argues that Buonanni rejected a conformity of causes in nature, which in turn informed his approach to natural history. His unique approach helped to transform Kircher’s collection from a cabinet of wonders to one of the earliest examples of the modern museum.