The aim of this work was to investigate the possibility of modifying the physical properties of indium tin oxide (ITO) layers by annealing them in different atmospheres and temperatures. Samples were annealed in vacuum, air, oxygen, nitrogen, carbon dioxide and a mixture of nitrogen with hydrogen (NHM) at temperatures from 200 °C to 400 °C. Annealing impact on the crystal structure, optical, electrical, thermal and thermoelectric properties was examined. It has been found from XRD measurements that for samples annealed in air, nitrogen and NHM at 400 °C, the In2O3/In4Sn3O12 share ratio decreased, resulting in a significant increase of the In4Sn3O12 phase. The annealing at the highest temperature in air and nitrogen resulted in larger grains and the mean grain size increase, while vacuum, NHM and carbon dioxide atmospheres caused the decrease in the mean grain size. The post-processing in vacuum and oxidizing atmospheres effected in a drop in optical bandgap and poor electrical properties. The carbon dioxide seems to be an optimal atmosphere to obtain good TE generator parameters-high ZT. The general conclusion is that annealing in different atmospheres allows for controlled changes in the structure and physical properties of ITO layers.