Although single-crystal X-ray diffraction is a proven technique to determine the structure of monolayer-protected coinage metal clusters in solid state, it is not readily applicable to the characterization of such cluster structures in solution. The complexity of the characterization problem increases further when intercluster reactions are studied, in which two reactive cluster ions interact to form final products using a sequence of structural changes involving exchange of metal atoms and ligands. Here, we present the first time-resolved structural study of such processes which occur when solutions of [TOA]+[Au25(PET)18]- and [PPh4]4 4+[Ag44(FTP)30]4- react upon mixing (PET: phenylethanethiolate; FTP: 4-fluorothiophenolate; and TOA: tetraoctylammonium ion). This is achieved using high-resolution trapped ion mobility mass spectrometry (TIMS). Specifically, we have used electrospray transfer to the TIMS apparatus followed by ion mobility measurements to probe the time-dependent structure of mass-selected AuxAg44-x(FTP)30 4- (x = 0-12) exchange products, with limited FTP for PET exchanges, formed in the reaction medium. Over the roughly 40 min reaction time before equilibration, with a product distribution centered around Au12Ag32(FTP)30 4-, we observe intermediate species, AuxAg44-x(FTP)30 4-, whose collision cross sections (CCSs) at a given x increase first relative to that of the Ag44(FTP)30 4- parent and decrease subsequently. We attribute this to an energy-driven migration of the incorporated Au atoms from the ligated "staples" at the cluster surface to its icosahedral core. Upon collisional heating of AuxAg44-x(FTP)30 4-, analogous back-migration of the heavier Au atoms from the core to the staples was observed in tandem mass spectrometry. To support our experimental observations, several isomeric structures (with all ligands) were calculated using density functional theory, and their CCS values were modeled using trajectory method calculations. © 2019 American Chemical Society.