Synchrotron X-ray total scattering measurements and accompanying pair distribution function (PDF) analyses are an excellent characterization technique to complement both transmission electron microscopy (TEM) and extended X-ray absorption fine structure (EXAFS) spectroscopy methods for detailed structural studies of atom-precise metal clusters. Herein, we study the thermal activation of Au25(SR)18- and Ag25(SR)18- clusters on alumina supports via in situ differential PDF (dPDF) analyses to compare structural changes in the metal clusters upon thermal activation in air. The metal-metal interatomic distances in Au25(SR)18- and Ag25(SR)18- clusters as measured by the dPDF method are comparable with those measured via single-crystal crystallographic and EXAFS methods. Compared to EXAFS analysis, in situ dPDF data can also provide high-temperature, non-element specific, longer range structural information with excellent temporal resolution. TEM and dPDF results show that Ag25(SR)18 systems behave significantly differently than analogous Au25(SR)18 systems upon thermal activation. Atom-precise Au clusters on alumina supports show continuous growth in particle size with increasing activation temperature due to particle coalescence upon thermal deprotection, and grow to an average size of 11.2 ± 2.1 nm for samples thermally activated at 650 °C. Conversely, analogous Ag clusters on alumina supports show particle size growth to mid-sized particles (3.2 ± 0.4 nm) at activation temperatures of 450 °C, beyond which the Ag particles then undergo thermal degradation to give smaller Ag clusters with an average size of 1.4 ± 0.2 nm for samples thermally activated at 650 °C. The significant difference in the behaviours of atom-precise, thiolate-protected Au and Ag clusters upon thermal activation emphasizes the development of distinct activation protocols for different metal cluster systems.