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The ability of plants to take up phosphorus (P) from soil depends on root morphology and root exudates release and can be modulated by beneficial soil microbes. These microbes can solubilize P, affect root elongation and branching, and lead to a higher uptake of P and other nutrients. However, coordination of these mechanisms is unclear, especially the mechanism for changing the available form of P. We aimed to dissect the effects of two different beneficial microbial taxa (plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF)) on root morphological traits, plant nutrient content, and growth in tomato and corn fertilized with either Gafsa rock phosphate (RP) or triple superphosphate (TSP), which have contrasting solubility levels. Tomato and corn were grown in pots and inoculated with one of three PGPB species or a mix of two AMF species or were not inoculated. Root traits, botanical fractions, and the contents of various mineral nutrients were measured. TSP stimulated tomato biomass accumulation compared to RP but did not stimulate corn biomass accumulation. PGPB improved the growth of both plant species under RP, with limited differences among the strains, whereas AMF only improved tomato growth under TSP. These differences between microbial systems were explained by a bacterial effect on the total root length but not on the mean root diameter and by the ability of AMF to improve the mineral nutrient content. The effects of PGPB were less dependent on the plant species and on P form than the effects of AMF.These results have implications for the improvement of the early plant growth through the management of beneficial microbes.