For applications in energy harvesting and environmentally friendly cooling, and for power sources in remote or portable applications, it is desired to enhance the efficiency of thermoelectric materials. One strategy consists of reducing the thermal conductivity while increasing or retaining the thermoelectric power factor. An approach to achieve this is doping to enhance the Seebeck coefficient and electrical conductivity, while simultaneously introducing defects in the materials to increase phonon scattering. Here, we use Mg ion implantation to induce defects in epitaxial ScN (111) films. The films were implanted with Mg+ ions with different concentration profiles along the thickness of the film, incorporating 0.35 to 2.2 at. % of Mg in ScN. Implantation at high temperature (600 °C), with few defects due to the temperature, does not substantially affect the thermal conductivity compared to a reference ScN. Samples implanted at room temperature, in contrast, exhibited a reduction of the thermal conductivity by a factor of 3. The sample doped with 2.2 at. % of Mg also showed an increased power factor after implantation. This paper thus shows the effect of ion-induced defects on thermal conductivity of ScN films. High-temperature implantation allows the defects to be annealed out during implantation, while the defects are retained for room-temperature implanted samples, allowing for a drastic reduction in thermal conductivity.