Ptychographic X-ray computed tomography was used to image nanoporous gold samples, with and without metal oxide additives, following incremental ex situ annealing steps up to 750 °C. Studying the exact same sample volumes following sequential annealing steps allowed accurate 3D imaging of large meso- and macropore systems over extended sample volumes. Extraction of surface area, pore size distribution, and pore connectivity were demonstrated using a skeletonization method. These properties are relevant in the study of functional materials such as catalysts which rely on diffusion processes within the pores. Samples with metal oxide additives were found to be more resistant to thermal annealing and gold ligament coarsening up to 550 °C, while pure nanoporous gold showed a greater loss of specific surface area during the same treatment. An anomalous stabilisation effect was observed during measurements in ambient air, with minimal coarsening observed in sample regions previously exposed to X-rays, and extensive coarsening in neighbouring regions of the same sample which were not previously exposed to X-rays. Thermal annealing of duplicate samples under nitrogen flow eliminated this effect, suggesting the possible formation of a protective surface structure induced by X-ray irradiation of nanoporous gold in air. The same observations may not be visible to conventional bulk sorption or porosimetry methods, showing the benefits of X-ray tomography for quantitative spatially-resolved imaging of porous nanomaterials.