The assembly and morphology of pores determine thermodynamic, flow and reactive properties of confined fluids. However, there is a limited understanding of how pore architectures dynamically develop in engineered and natural materials. To develop a calibrated understanding of fluid properties in confinement, the synthesis of architected materials has been proposed. The design of geo-architected materials has to be informed by the dynamic evolution of the morphology in response to thermal or chemical events. In this study, we probe thermally induced morphological evolution of spherical silica nanoparticles 220 ± 30 nm in diameter using in-operando Ultra-Small and Small Angle X-Ray Scattering measurements. The calcination experiments demonstrated that at temperatures up to 600 °C the pore radii remained in the range of 2.15 nm–2.35 nm and the particle diameters in the range of 220 ± 30 nm. Sintering these calcined silica nanoparticles to temperatures up to 1050 °C reduced the pore size from 2.2 ± 0.1 nm to ∼1.8–0.2 nm. These changes corresponded to the formation of siloxane (Si-O-Si) bridges resulting from dehydroxylation. The characteristic pore radius of sintered particles was also confirmed by N2 adsorption measurements. These studies represent the use of non-invasive dynamic characterization methods such as X-ray scattering to elucidate thermally induced morphological evolution in architected siliceous materials.