Controlling the generation of secondary phases is crucial to enhance the thermoelectric performance of any material. In this manuscript, we have demonstrated the modulation of thermoelectric properties of Al and Sn doped ZnO nano particles by the post annealing method. Al doped ZnO (ZAO) and Sn doped ZnO (ZTO) nano particles were synthesized by the simple hydrothermal technique. After growth, both samples were annealed at 800 °C for 1 h. The Seebeck data suggested that the annealed ZTO sample has the highest value of Seebeck coefficient as compared to its counterpart as grown and ZAO samples as well. This highest value of Seebeck coefficient is related to generation of secondary phases in annealed ZTO. The generation of secondary phases was also causing an enhancement in mobility of the carriers. This carriers, mobility enhancement resulted in the high electrical conductivity value for ZTO sample leads to the highest value of power factor for ZTO about 1.2 × 10-4 Wm-1K-2. The XRD data confirmed that ZAO samples have better crystal quality as compared to ZAO samples. The poor crystal quality of ZTO is due the presence of SnO based secondary phases. For further verification of this argument, we have performed Raman spectroscopy and SEM measurements which supported our proposed argument.