The problem with waste heat in solar panels has stimulated research on materials suitable for hybrid solar cells, which combine photovoltaic and thermoelectric properties. One such potential material is Cu2ZnSnS4(CZTS). Here, we investigated thin films formed from CZTS nanocrystals obtained by “green” colloidal synthesis. The films were subjected to thermal annealing at temperatures up to 350 °C or flash-lamp annealing (FLA) at light-pulse power densities up to 12 J/cm2. The range of 250–300 °C was found to be optimal for obtaining conductive nanocrystalline films, for which the thermoelectric parameters could also be determined reliably. From phonon Raman spectra, we conclude that in this temperature range, a structural transition occurs in CZTS, accompanied by the formation of the minor CuxS phase. The latter is assumed to be a determinant for both the electrical and thermoelectrical properties of CZTS films obtained in this way. For the FLA-treated samples, the film conductivity achieved was too low to measure the thermoelectric parameters reliably, although the partial improvement of the CZTS crystallinity is observed in the Raman spectra. However, the absence of the CuxS phase supports the assumption of its importance with respect to the thermoelectric properties of such CZTS thin films.