Several recent reports have highlighted some of the mechanisms involved in the enhanced tolerance to abiotic stresses induced by root-associated microorganisms, although additional efforts are still required to exploit and optimize these strategies. Particularly, arbuscular mycorrhizal fungi (AMF) play an important role as “bio-fertilizing microorganisms”, establishing mutualistic symbioses with the roots of most crops. In this work, different microbial inocula (a single AMF species, a combination of three different AMF species, a combination of two plant growth-promoting bacteria (PGPB) strains and a more complex commercial inoculum) have been used to inoculate tomato plants (cv San Marzano nano), in order to verify their effects on the tolerance to a water deficit condition in pots, through the evaluation of biochemical stress markers and hormonal profiles (ABA and IAA). Results showed differences among tomato responses to water limitation depending on microbial inocula, confirming the importance to characterize the optimal plant/microorganism genotype combination(s) to maximize plant performance and tolerance. These findings open new perspectives for a better exploitation of these microorganisms.