Microbial communities in the rhizosphere carry out fundamental processes that can improve plant growth by competing with root pathogens as well as enhancing nutrient availability. In the present study, root inoculation of tomato cultivar 'Formula' with Bacillus amyloliquefaciens and Glomus intraradices was applied in two experiments. In the first experiment, these inoculants were applied in non-grafted 'Formula' plants to test their impact on nutrient uptake, yield, and protection from Fusarium oxysporum f. sp. lycopersici. The second experiment addressed the impact of these two inoculants on nutrient uptake and yield in 'Formula' plants either self-grafted or grafted onto the rootstock 'He-man'. Application of B. amyloliquefaciens increased appreciably the fruit yield in the first experiment by raising the fruit number per plant, while restricting colonization of F. oxysporum f. sp. lycopersici. In the second experiment, the population density of B. amyloliquefaciens on the roots of 'He-man' was higher than on those of 'Formula', while that of G. intraradices was not influenced by the tested root genotypes. The vegetative fresh and dry shoot biomass was not influenced by application of B. amyloliquefaciens or G. intraradices but was significantly enhanced by grafting 'Formula' onto 'He-man' in comparison with self-grafting of 'Formula'. Both B. amyloliquefaciens and G. intraradices enhanced significantly the fruit yield by increasing the total fruit number per plant, whereas the mean fruit weight was not influenced by any treatment. Grafting had no impact on fruit yield and yield components. Root inoculation with G. intraradices increased the fruit P, regardless of the root genotype, as well as the fruit Ca and Mg in plants grafted onto 'He-man', in comparison with non-inoculation.