The use of pulsed microwave discharges is examined as a way to improve nanocrystalline diamond film growth process, while maintaining small amounts of hydrogen in the argon-based gas mixture in order to ensure plasma stability. The effects of pulse repetition rate and duty cycle on the film properties are investigated, keeping a constant time-average microwave power of 500 W at 20,000 Pa. When the duty cycle is maintained at 50%, the best microstructure and topography properties are obtained at low pulse repetition rate (50 Hz), with a 10 nm grain size and a 25 nm Rms roughness, which is better by a factor of two than the values reached in conventional continuous mode while the growth rate is comparable. At low frequency (50 Hz), possible variations of duty cycle in the range 50–80% has only a weak influence, so that films with optimal properties and growth rate are always provided. Besides, the measured and calculated time-average gas temperature for pulsed discharges as a function of duty cycle, and for continuous plasmas, yield roughly constant and identical values close to 4000 K. This points out that no changes in the heating or cooling of the reactor walls and substrate are required when the pulsed mode is employed, even if the injected peak power may be greatly changed in order to keep constant time-average values.