The SrTiO3 thin films were fabricated by pulsed laser deposition. Subsequently ion implantation with 60 keV N ions at two different fluences 1 × 1016 and 5 × 1016 ions/cm2 and followed by annealing was carried out. Thin films were then characterized for electronic structure, morphology and transport properties. X-ray absorption spectroscopy reveals the local distortion of TiO6 octahedra and introduction of oxygen vacancies due to N implantation. The electrical and thermoelectric properties of these films were measured as a function of temperature to understand the conduction and scattering mechanisms. It is observed that the electrical conductivity and Seebeck coefficient (S) of these films are significantly enhanced for higher N ion fluence. The temperature dependent electrical resistivity has been analysed in the temperature range of 80–400 K, using various conduction mechanisms and fitted with band conduction, near neighbour hopping (NNH) and variable range hopping (VRH) models. It is revealed that the band conduction mechanism dominates at high temperature regime and in low temperature regime, there is a crossover between NNH and VRH. The S has been analysed using the relaxation time approximation model and dispersive transport mechanism in the temperature range of 300–400 K. Due to improvement in electrical conductivity and thermopower, the power factor is enhanced to 15 µWm−1 K−2 at 400 K at the higher ion fluence which is in the order of ten times higher as compared to the pristine films. This study suggests that ion beam can be used as an effective technique to selectively alter the electrical transport properties of oxide thermoelectric materials.