In this manuscript, we have explored the potential of Copper Zinc Tin Sulfide (CZTS) nano-crystals for thermoelectric power generation application by the engineering of secondary phases. CZTS nano-crystals were grown on various substrates (crystalline silicon (c-Si), multi-crystalline silicon (mc-Si), Soda Lime Glass (SLG) and Indium Tin Oxide (ITO) coated glass) using sol-gel solution technique. The grown samples were sulphurized in tube furnace at 500C for 20 min under vacuum. It was observed that sample grown on mc-Si has highest Seebeck coefficient of 667 μV/0C while sample grown on ITO substrate has the lowest value of Seebeck coefficient (70 μV/0C) at measurement temperature 100 °C. The reported high Seebeck coefficient of CZTS/mc-Si sample is related to the emergence of secondary phases. To verify this argument, we have performed XRD, Raman spectroscopy and UV/Visible measurements. XRD data revealed the presence of (112), (103) and (220) phases of CZTS in all samples but CZTS/mc-Si and CZTS/c-Si samples demonstrated additional phases related to secondary phases. Raman spectroscopy was also used to verify the presence of secondary phases in CZTS/mc-Si. Raman measurements showed that all samples consisted of CZTS vibration mode at 329 cm−1 but CZTS/mc-Si and CZTS/c-Si have additional secondary phases due to CuxS, CuSnS and SnxS vibration modes. UV–Vis data also verified our argument that Seebeck coefficient was enhanced due to secondary phases engineering using various substrates for CZTS growth.