The effect of temperature on microstructure and optical properties of nanocomposite films containing Ag nanoparticles embedded in a polymer matrix of Teflon AF was investigated in detail. Temperature effects were studied in two modes: the effect of temperature during preparation of the nanocomposites and post-deposition heat treatment. Substrate heating during deposition leads to a decrease in the condensation coefficient up to the glass transition temperature of the polymer and increases beyond this temperature. During heat treatment after deposition metal diffuses into the polymer and leads to a change in the microstructure of the nanocomposites resulting in larger metal cluster size, an increase in the interparticle distance and more spheroidal shaped clusters. An increase in the substrate temperature during deposition can lead to both blue shifts and red shifts of the plasmon peak position. Changes in the microstructure upon heat treatment above the glass transition temperature are caused by diffusion of metal clusters into the polymers. In this regime, the peak wavelength of the plasmon band shifts towards shorter wavelength with increasing temperature.