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The aim of the current study wat to comparatively assess the impact of different nitrogen (N) fertilization schemes on fresh pod yield and yield quality in either organically or conventionally grown common beans (Phaseolus vulgaris L.). Prior to common bean crop establishment, the experimental field site was cultivated following either organic (a) or conventional (b) farming practices with a winter non-legume crop (Brassica oleracea var. italica) (BR), or (c) with field bean (Vicia faba sp.) destined to serve as a green manure (GM) crop. At the end of the winter cultivation period the broccoli crop residues (BR) and green manure biomass (GM) were incorporated into the soil and the plots that accommodated the treatments (a) and (c) were followed by an organically cultivated common bean crop, while the conventional broccoli crop was followed by a conventionally cropped common bean crop. Additional to the plant residues (BR), sheep manure (SM) at a rate of 40 kg N ha−1 was also applied to the organically treated common beans, while the plots with a conventionally cropped common bean received 75 kg N ha−1. Organic common bean treated with SM + BR produced smaller pods of higher dry matter and bioactive compound content, responses that are correlated with limited soil N availability. No significant variations were observed on yield components and N levels of pods cultivated under organic (SM + GM) and conventional cropping systems. Pod sugar and starch content was not influenced by the different fertilization practices. In conclusion, we have demonstrated that the combined application of SM + GM can be considered as an efficient N-fertilisation strategy for organic crops of common bean, benefiting their nutritional value without compromising yield.