In multicomponent thin films, properties and functionalities related to post-deposition annealing treatments, such as thermal stability, optical absorption and surface morphology are typically rationalized, neglecting the role of the substrate. Here, we show the role of the substrate in determining the temperature dependent behaviour of a paradigmatic two-component nanogranular thin film (Ag/TiO2) deposited by gas phase supersonic cluster beam deposition (SCBD) on silica and sapphire. Up to 600 °C, no TiO2 grain growth nor crystallization is observed, likely inhibited by the Zener pinning pressure exerted by the Ag nanoparticles on the TiO2 grain boundaries. Above 600 °C, grain coalescence, formation of However, the two substrates steer the evolution of the film morphology and optical properties in two different directions. anatase and rutile phases and drastic modification of the optical absorption are observed. On silica, Ag is still present as NPs distributed into the TiO2 matrix, while on sapphire, hundreds of nm wide Ag aggregates appear on the film surface. Moreover, the silica-deposited film shows a broad absorption band in the visible range while the sapphire-deposited film becomes almost transparent for wavelengths above 380 nm. We discuss this result in terms of substrate differences in thermal conductivity, thermal expansion coefficient and Ag diffusivity. The study of the substrate role during annealing is possible since SCBD allows the synthesis of the same film independently of the substrate, and suggests new perspectives on the thermodynamics and physical exchanges between thin films and their substrates during heat treatments.