Aims Plants host communities of fungal and bacterial endophytes, establishing a complex network of multipartite interactions, but the mechanisms whereby they interact are poorly understood. Some fungi, such as the beneficial mycorrhiza-like fungus Serendipita (=Piriformospora) indica, can be helped by bacteria for establishment, survival and colonization. Although this fungus harbors a Rhizobium as an endofungal bacterium, we hypothesized that other bacteria might also establish associations with the fungus and combining S. indica with bacteria might enhance plant growth and health. Methods The interactions among S. indica and four endophytic Proteobacteria belonging to Methylobacterium, Tardiphaga, Rhodanobacter and Trinickia spp. were characterized in vitro and for their effect on tomato growth and biocontrol of Fusarium oxysporum and Rhizoctonia solani. Possible mechanisms behind these interactions were described based on genome and microscopic analyses, using fungal and bacterial strains tagged with fluorescent markers. Results All bacteria stimulated S. indica growth in vitro. Moreover, several of the bacteria stimulated growth of tomato plants, but co-inoculations with S. indica and bacteria did not perform better than single inoculations. Contrarily, combinations of S. indica and bacteria significantly reduced disease progression of fungal pathogens. These microbes seem to cooperate in the process of root colonization for instance by increasing fungal sporulation and hyphae expansion, showing multipartite interaction between microbes and plants. Interestingly, the strain of Trinickia internally colonizes spores of S. indica as an endofungal bacterium during in vitro-co-culturing, suggesting further that the fungus might acquire formerly unrecognized genera of bacteria and genome analysis of the bacteria revealed many genes potentially involved in fungal and plant growth stimulation, biocontrol and root colonization, highlighting putative mechanisms of plant-fungal-bacterial interaction. Conclusions Our study represents an important step towards unraveling the complex interactions among plants, S. indica, endophytic bacteria and fungal pathogens, and indicates that adding bacteria to fungal inoculum could have a remarkable impact on the plant-S. indica symbiosis.