In this study, the structural integrity of mullite (3Al2O3·2SiO2) films, deposited on silicon carbide (SiC) substrates using chemical vapor deposition (CVD), was investigated via increasing load nanoscratch tests. The films were configured by mullite columns of stoichiometric composition growing from a silica-rich layer in contact with the SiC substrate. Controlled damage was induced in the 3Al2O3·2SiO2 films at relatively low scratch loads. Radial and lateral cracking were applied until final delamination and repeated chipping were achieved as the load increased. The intrinsic integrity of the 3Al2O3∙2SiO2 film and the performance of the coated 3Al2O3·2SiO2/SiC system, regarded as a structural unit, were analyzed. With the aid of advanced characterization techniques at the surface and subsurface levels, the configuration and morphology of the damage induced in the coated system by the nanoscratch tests were characterized, and the scratch damage micromechanisms were identified. Finally, the adhesion of the film, in terms of energy of adhesion and interfacial fracture toughness, was determined using different models proposed in the literature. The results from this investigation contribute to the understanding of the mechanical performance and structural integrity of EBC/SiC-based systems, which over the past few years have increasingly been implemented in novel applications for gas turbines and aircraft engines.