Monolayer protected clusters exhibit rich diversity in geometric and electronic structures. However, structure-reactivity relationships in these clusters are rarely explored. In this context, [Ag44(SR)30]4-, where -SR is an alkyl/aryl thiolate, is an interesting system due to its geometrically and electronically closed-shell structures and distinct charge states. We demonstrate that these structural features of [Ag44(SR)30]4- are distinctly manifested in its solution-state reaction with another cluster, [Au25(SR)18]-. Through this reaction, an alloy cluster anion, [Au12Ag32(SR)30]4-, evolves spontaneously as revealed by high-resolution electrospray ionization mass spectrometry. Ultraviolet-visible absorption spectroscopy and density functional theory calculations indicate that [Au12Ag32(SR)30]4- is formed by the substitution of all of the Ag atoms in the innermost icosahedral shell of [Ag44(SR)30]4- and the abundance is attributed to its higher stability due to closed geometric as well as electronic shell structure, similar to the reactant clusters. We further demonstrate that the substitution of metal atoms in the middle dodecahedral shell and the outermost mount sites are also possible, however such substitutions produce AuxAg44-x(SR)30 alloy clusters with geometrically and electronically open shells. Depending on specific sites of substitution, an unexpected superatom-nonsuperatom transition occurs in the distribution of AuxAg44-x(SR)30 alloy clusters formed in this reaction. Our results present a unique example of a structure-reactivity relationship in the metal atom substitution chemistry of monolayer protected clusters, wherein a systematic trend, reflecting the geometric and the electronic shell structures of the reactant as well as the product clusters, was observed. © 2017 American Chemical Society.