Biological supramolecules offer attractive templates for nanoparticle synthesis and nanodevice fabrication because of their precise size and shape. Viruses in particular have gained significant attention in nanodevice fabrication for applications such as nanoelectronics, batteries, catalysis, and sensing. However, the performance range of these viral-nanoparticle complexes is not well known because of the lack of fundamental studies on their properties. In this work, we employ in situ grazing incidence small-angle X-ray scattering (GISAXS) to examine the thermal stability of viral-nanoparticle complexes composed of tobacco mosaic virus (TMV) and palladium nanoparticles. Specifically, we show that the stability of the Pd nanoparticles on TMV is significantly enhanced as compared to that of particles on the solid substrate surface. Furthermore, we show that the agglomeration of Pd nanoparticles and the degradation of the TMV templates are coupled and occur simultaneously. These results demonstrate a potent methodology toward the in situ analysis of subtle changes in viral-nanoparticle complexes in dynamic environments. We envision that the results and methodology demonstrated in this study could be applied to better understand the properties and dynamic behaviors of organic-inorganic hybrid materials and nanodevices in various applications.