Ion implantation is a widely used technique to introduce defects in low-dimensional materials and tune their properties. Here, we investigate the thermoelectric properties of scandium nitride thin films implanted with helium ions, revealing a positive impact of defect engineering on thermoelectric performance. Transport properties modeling and electron microscopy provide insights on the defect distribution in the films. The electrical resistivity and Seebeck coefficient increase significantly in absolute values after implantation and partially recover upon annealing as some of the implantation-induced defects heal. The thermal conductivity decreases by 46 % post- implantation due to the formation of extended defects and nanocavities. Consequently, the thermoelectric figure of merit zT doubles for the sample annealed at 673 K. These findings highlight the potential of controlled ion implantation to enhance thermoelectric properties in thin films, paving the way for further optimization through defect engineering.