In vitro antagonistic effect of various PGPR namely A. chroococcum, B. megaterium, B. circulans, B. subtilis, Ps. fluorescens and T. viride against F. solani or R. solani was determined. Results observed that using all PGPR strains suppressed F. solani and R. solani. The inhibition zone increased by increasing incubation time. Under greenhouse condition, onion inoculation with investigated PGPR strains reduced disease severity of F. solani by rate ranging between (79.4-93.5%). However, they reduce disease severity of R. solani by rate ranging between (84.5-93.6%). Accordingly, the rate of disease incidence reduced by the range between (68.4-81.8%) and (65.5-81.8%) in case of infested with F. solani and R. solani respectively. Moreover, they had positive effect on plant defense enzymes, nutrients uptake and growth parameters. In farm of the Central Laboratory of Organic Agriculture, Giza station, ARC Giza, Egypt, the open field experiment was carried out to study the integrated effect of biofertilizing-PGPR and biocontrol agents with compost to improve green onion growth characteristics and yield under the organic agriculture system. During the experiment the soil microbial enzymes activity, total NPK and plant uptake, defense enzymes activity, growth characteristics and vegetative yield were estimated. Data obtained showed that onion treated with compost + biofertilizing-PGPR + B. subtilis + T. viride (T7) gave the highest values of in all estimated parameters except defense enzymes activity. So, it can be recommended as integrated fertilizing program to promote green onion growth, increase crop production, and decrease production costs.