Si-diffusion from Si-based substrates into yttria-stabilized-zirconia (YSZ) thin films and its impact on their microstructure and chemistry is investigated. YSZ thin films used in electrochemical applications based on micro-electrochemical systems (MEMS) are deposited via spray pyrolysis onto silicon-based and silicon-free substrates, i.e. Si x N y -coated Si wafer, SiO2 single crystals and Al2O3, sapphire. The samples are annealed at 600°C and 1000°C for 20h in air. Transmission electron microscopy (TEM) showed that the Si x N y -coated Si wafer is oxidized to SiO z at the interface to the YSZ thin film at temperatures as low as 600°C. On all YSZ thin films, silica is detected by X-ray photoelectron spectroscopy (XPS). A particular large Si concentration of up to 11at% is detected at the surface of the YSZ thin films when deposited on silicon-based substrates after annealing at 1000°C. Their grain boundary mobility is reduced 2.5 times due to the incorporation of SiO2. YSZ films on Si-based substrates annealed at 600°C show a grain size gradient from the interface to the surface of 3nm to 10nm. For these films, the silicon content is about 1.5at% at the thin film's surface.