CrN-based thin films are emerging as thermoelectric materials for energy harvesting. Their thermoelectric properties depend on phase composition and stoichiometry, necessitating control over the nitrogen content and how it affects the phase composition. Here, the effect of high-temperature ammonia annealing on the thermoelectric properties as well as crystal structure of thin films of Cr–N on c-plane sapphire (Al2O3(0001)) was investigated. Single-phase (cubic CrN) and mix-phase (cubic CrN + hexagonal-Cr2N) Cr–N films were annealed in ammonia, converting any secondary phase of hexagonal Cr2N to cubic CrN. The thermoelectric properties of the films that contained a secondary phase of hexagonal Cr2N greatly improved upon annealing, with an increase of 900% to 0.5 × 10–3 W m–1 K–2 for the film annealed at 800 °C for 2 h. Annealing of single-phase films of cubic CrN resulted in films with near-insulating electrical properties. For the thermoelectric applications of CrN, ammonia annealing can be beneficial over meticulous deposition control.