In recent decades the knowledge of nitrous oxide (N2O) emissions after the application of nitrogen (N) fertilizers in agriculture soil has improved. However the understanding of emissions of N2O from Canadian organic agricultural systems has not been developed. The Glenlea Long Term Crop Rotation is the longest running organic conventional comparison study in western Canada and was used here to compare N2O emissions between the systems. In organic cropping systems forage legumes such as alfalfa are incorporated into the soil as an N source. The amount of N2O that is emitted after the incorporation and during the subsequent crop is not well known. The wheat and legume phases (alfalfa (Medicago sativa) in organic system and soybean (Glycine max L.) in the conventional) of the rotation were monitored for N2O. In 2014, 2015, and spring 2016 (data still being analysed) emissions of N2O were monitored using the vented static chambers method as well, soil conditions (temperature, moisture, inorganic N and extractable carbon) and yields were measured. Typical N2O emissions from spring applied urea were observed after application in the conventional system however no emission episode was seen after the fall alfalfa plough down or during spring thaw in the organic system. Greater NO3- accumulation was observed in the organic treatments however low emissions were observed. The organic system resulted in lower yields for both years, but still resulted in lower emissions per amount of grain produced (yield-scaled emissions) than the conventional system. This study adds to the knowledge that N2O emissions from organic systems do differ from conventional however yields need to be improve to fully exploit the benefits.