The use of beneficial microorganisms, such as plant growth promoting rhizobacteria (PGPR) and mycorrhizal fungi, for organic farming could improve the productivity and the resilience of vegetable crops. Both PGPR and PGPF are allowed for organic farming, and they represent new important tools for regenerating poor and marginal soils in transition to environmentally friendly farming. In the experiment, the effects of PGPM-based products were evaluated on snap bean in combination with two irrigation regimes. The experimental design adopted was split-plot, with the main plot represented by the irrigation regime (reintegration of 100 and 60% of the ETc), the sub-plot by the microbial consortia, and finally the sub-sub-plot by genotype (‘Domino’ and ‘Maxi’). Seeds were sown in a cold greenhouse and the growing cycle finished after 86 days from sowing. The results showed a significant increase of the yield due to the application of PGPM compared to the control. The deficit irrigation applied (ETc 60%) affected plants growth in the two genotypes and their related production differently (in average 2.20 kg m−2 for Domino and 3.63 kg m−2 for Maxi), showing a positive effect of PGPM on yield (in average 2.47 kg m−2 without PGPM and 3.36 kg m−2 with PGPM) and product quality. Furthermore, an interesting negative correlation between the number of nodules and the yield was also observed, as a consequence of their early outcome which increased plant productivity in relation to the experimental factors.