Deposition of diamond layers in a CH4-CO2 microwave discharge operating in pulsed mode was achieved. The effects of nitrogen addition and microwave power modulation on the plasma reactivity were studied by time resolved optical emission spectroscopy. An enhancement of the molecular dissociation during the early stage of the pulse has been observed. The resulting diamond layers showed less graphite contamination as compared with that obtained in continuous discharge. Furthermore, the addition of nitrogen to the discharge operating in this pulsed mode further decreases the graphite contamination and improves crystallization due to reduction of secondary germination.