Legume crops constitute an essential component of rotations in organic farming systems due to their ability to provide plant available nitrogen to agricultural ecosystems arising from symbiotic N2 fixation. However, there is a general need to increase grain legume protein production in Europe so as to meet the increasing demand while reducing resource utilization, thereby contributing to mitigation of global climate change. Taking this need into consideration, a field-based experiment with pea (Pisum sativum L.) was carried out in a field certified for organic agriculture from November 2014 to June 2015. The experiment was laid out in a split-plot design with two main treatments (conventional and organic farming system) and four sub-plots per main plot corresponding to four different pea genotypes, particularly one commercial cultivar ('Onward'), and three local landraces ('Amorgos', 'Andros' and 'Schinousa'). Standard inorganic fertilizer (11-15-15, N:P2O5:K2O) and sheep manure were used as base dressings in the conventional and the organically-treated plots, respectively. The aim of the experiment was to test the performance of each pea genotype in organic farming crops as compared to conventional cropping, in terms of: green seed yield, and greenhouse gas (GHG) emissions. The results of this study indicate that 'Andros' increased significantly the above-ground biomass and the fresh green seed production on the harvesting date when compared with all the other genotypes. In addition, there were significant differences in cumulative N2O fluxes between the pea cultivars with 'Schinousa' producing the highest N2O amounts and 'Andros' the lowest. In conclusion, the pea genotype seems to have a strong influence on both GHG emissions and production and therefore, appropriate selection of cultivars is imperative for efficient use of this legume in organic cropping systems.