Rice blast is one of the most destructive rice diseases known to cause considerable yield losses globally. Plant growth promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) are closely associated with rice plants and improve plant growth and health. To determine how isolated bacteria trigger rice growth, an assessment of phosphate solubilization and auxin production mechanisms was carried out in vitro and in vivo. In this study, the interactions between PGPR and Rhizophagus irregularis were evaluated in wildtype and CYCLOPS mutant plants to provide a sustainable solution against blast disease and reduce the amount of yield loss. Importantly, Bacillus subtilis UTSP40 and Pseudomonas fluorescens UTSP50 exhibited a suppressive effect on AMF colonization which shows the probable existence of a functional competition between AMF and PGPR to dominate the rhizosphere. On the other hand, R. irregularis decreased the biocontrol activity of B. subtilis UTSP40 in wild type, although this reduction was not significant in mutant plants. Results showed that the same defense-related genes were induced in the roots of wild type colonized by B. subtilis UTSP40 and R. irregularis. Therefore, plant cell programs may be shared during root colonization by these two groups of beneficial microorganisms.