In current study, two successive experiments were carried out during 2014 and 2015 at the Experimental Research Farm, Sakha Horticulture Station, Kafr El-Sheikh. Eleven treatments included combinations with N, P and K microbial inoculants and 1/3 or 2/3 or 100% of N, P and K-mineral fertilizers. The effect of mineral combined with bio-fertilizers on quality and productivity of green onion under salt-affected soils has been investigated as well as on soil microbial enzyme activities. In general the highest values of soil dehydrogenase and alkaline phosphatase activities were 27.0 and 35.3 µg TPF g^-1 dw h^-1 and 20.9 and 15.0 µg ρ NP g^-1 h^-1, respectively in both seasons using of the combination of these fertilizers (NPK-biofertilizers combined with 100% NPK-mineral fertilizers). Concerning vegetative growth parameters and total yield, NPK-microbial inoculants combined with 100% NPK-mineral fertilizers had the highest values. There were not significant differences in the most cases between N -microbial inoculants combined with 100% NPK-mineral fertilizers and PK-microbial inoculants combined with 100% NPK-mineral fertilizers, comparing with 2/3 NPK-mineral fertilizers + NPK- microbial inoculants. Total chlorophyll content was reduced by using biofertilizers alone (NPK-microbial inoculants alone). Moreover, using biofertilizers led to relatively decrease soil salinity. The results of this study suggest that, it should be replaced the mineral fertilizers by biofertilizers, even partially, to produce a better food and such integrated nutrient management program should be addressed under salt-affected soils.