This work aims at experimentally assessing the effect of structural disorder and/or chemical interdiffusion on thermal boundary conductance (TBC) at metal/dielectric interfaces. To this end, the TBC of Au/Si and Ti/Si interfaces was measured by time domain thermoreflectance in the as-deposited state and after various heat treatments. Transmission electron microscopy (TEM) was used to determine the structure of the interface for each heat treatment condition. The TBC at the Au/Si interface was found to be highest in the as-deposited state and to be somewhat reduced after heat treatments. TEM images showed that the highest TBC was obtained when the interface contained a disordered transition layer with some degree of interdiffusion as present in the as-deposited state. Heat treatments led to the separation of species and to more abrupt interfaces with lower TBC. Whether this change in TBC was linked to disorder or to interdiffusion could not be distinguished. The TBC at the Ti/Si interfaces was observed to decrease with the heat treatment duration. TEM investigations revealed the presence of a thin disordered layer that did not evolve much with heat treatments. The evolution of the TBC was hence rationalized by interdiffusion facilitated by heat treatments that most likely modified the diffusion zone thickness and chemical composition, as well as the disordered layer's chemical composition. These changes result in modified interfacial properties, which ultimately affect the TBC. A quantitative exploration of the TBC dependence on the composition was not possible in this work, due to the extreme thinness of the regions under consideration preventing any reliable STEM-energy dispersive x-ray measurement. Published under license by AIP Publishing.