Modulating the structure-property relationship in atomically precise nanoclusters (NCs) is vital for developing novel NC materials and advancing their applications. While promising biphasic ligand-exchange (LE) strategies have been developed primarily to attain novel NCs, understanding the mechanistic aspects involved in tuning the core and the ligand-shell of NCs in such biphasic processes is challenging. Here, we design a single phase LE process that enabled us to elucidate the mechanism of how a hollow NC (e.g., [Ag44(SR)30]4-, -SR: thiolate) converts into a non-hollow NC (e.g., [Ag25(SR)18]-), and vice versa. Our study reveals that the complete LE of the hollow [Ag44(SPhF)30]4- NCs (–SPhF: 4-fluorobenzenethiolate) with incoming 2,4-dimethylbenzenethiol (HSPhMe2) induced distortions in the Ag44 structure forming the non-hollow [Ag25(SPhMe2)18]- by a disproportionation mechanism. While the reverse reaction of [Ag25(SPhMe2)18]- with HSPhF prompted an unusual dimerization of Ag25, followed by a rearrangement step that reproduces the original [Ag44(SPhF)30]4-. Remarkably, both the forward and the backward reactions proceed through similar size intermediates that seem to be governed by the boundary conditions set by the thermodynamic and electronic stability of the hollow and non-hollow metal cores. Furthermore, the resizing of NCs highlights the surprisingly long-range effect of the ligands which are felt by atoms far deep in the metal core, thus opening a new path for controlling the structural evolution of nanoparticles.