Structure-reactivity correlations in metal atom substitution reactions of three model monolayer-protected alloy clusters, Ag25-xAux(SR)18 (I), Au25-xAgx(SR)18 (II), and AuxAg44-x(SR)30 (III) where (-SR = alkyl/arylthiolate), are demonstrated. We show that the Au atoms of I and III and Ag atoms of II can be substituted by their reactions with the parent clusters Ag25(SR)18, Ag44(SR)30, and Au25(SR)18, respectively. Though these alloy clusters possess certain common structural features, they exhibit distinctly different reactivities in these substitution reactions. The Au of I and III and Ag of II at the outermost sites, i.e., M2(SR)3 staples of I and II and M2(SR)5 mounts of III, were substituted more easily compared to those at the inner, icosahedral sites. Au atoms at the icosahedral shell of I were completely substituted while Ag atoms of II at similar positions were not labile for substitution. This shows that the icosahedral shell of II is more rigid compared to that in I. We show that the Au atom in Ag24Au1(SR)18 cannot be substituted, which indicates that this Au atom is located at the center of the icosahedral shell. Similarly, when x ≤ 12, the Au atoms of III cannot be substituted, indicating that these atoms are located in the innermost icosahedral shell. In summary, our results demonstrate that metal atom substitution reactions correlate with the geometric structures of these clusters. © 2017 American Chemical Society.