Amorphous oxide semiconductors are promising new materials for various optoelectronic applications. In this study, improved electrical and optical properties upon thermal and microwave processing of mixed-oxide semiconductors are reported. First, arsenic-doped silicon was used as a model system to understand susceptor-assisted microwave annealing. Mixed oxide semiconductor films of indium zinc oxide (IZO) and indium gallium zinc oxide (IGZO) were deposited by room-temperature RF sputtering on flexible polymer substrates. Thermal annealing in different environments—air, vacuum and oxygen was done. Electrical and optical characterization was carried out before and after annealing. The degree of reversal in the degradation in electrical properties of the thin films upon annealing in oxygen was assessed by subjecting samples to subsequent vacuum anneals. To further increase the conductivity of the IGZO films, Ag layers of various thicknesses were embedded between two IGZO layers. Optical performance of the multilayer structures was improved by susceptor-assisted microwave annealing and furnace-annealing in oxygen environment without compromising on their electrical conductivity. The post-processing of the films in different environments was used to develop an understanding of mechanisms of carrier generation, transport and optical absorption. This study establishes IGZO as a viable transparent conductor, which can be deposited at room-temperature and processed by thermal and microwave annealing to improve electrical and optical performance for applications in flexible electronics and optoelectronics.