This study focuses on characterization and understanding of the substrate effect on Ge doped GaN thin films coated onto transparent substrates. The produced films were deposited onto unheated glass and unheated polyethylene terephthalate by using thermionic vacuum arc technique. Gallium nitride and germanium pellets were used in the thin film production. Reflectance, refractive index and thicknesses of Ge doped GaN thin films were measured by optical interferometer using Cauchy model for fitting. The transmittances were determined in the wavelength range between 200 and 1000 nm by using UV-Vis double beam spectrophotometer. The optical Tauc method was used to determine the band gap energies of produced thin films. Surface morphologies of produced thin films were characterized by atomic force microscopy and also field emission scanning electron microscopy. In conclusion, the substrate effect on the optical and morphological properties of the produced thin films was observed.