Cation exchange reactions of colloidal copper sulfide nanoparticles are widely used to produce derivative nanoparticles having unique compositions, metastable crystal structures, and complex heterostructures. The copper sulfide crystal structure plays a key role in the mechanism by which cation exchange occurs and the product that forms. Here, we show that digenite copper sulfide nanoparticles undergo a spontaneous phase transition to tetragonal chalcocite in situ, prior to the onset of cation exchange. Room-temperature sonication of digenite (Cu1.8S) in trioctylphosphine, a Lewis base that drives cation exchange, extracts sulfur to produce tetragonal chalcocite (Cu2S). The subtle structural differences between digenite and tetragonal chalcocite are believed to influence the accessibility of cation diffusion channels and concomitantly the mechanism of cation exchange. Structural relationships in nanocrystal cation exchange are therefore dynamic, and intermediates generated in situ must be considered.