Bacillus spp. are among the most efficient known plant growth-promoting rhizobacteria (PGPR). The PGPR Bacillus sp. strain RZ2MS9 is a multi-trait maize growth promoter previously isolated from guarana plants cultivated in the Amazon rainforest. However, there are several aspects of its interaction with the host that need further investigation. To achieve effective performance of microbial inoculants in crop production, it is necessary to monitor the plant’s colonization by a PGPR and to assess the potential synergy among beneficial strains. Here, we obtained a stable mutant of RZ2MS9 labelled with green fluorescent protein (RZ2MS9-GFP). We verified that the insertion of the plasmid did not affect either bacterial growth nor its ability to promote maize growth in vitro. Using fluorescent microscopy and qPCR, we demonstrated that RZ2MS9-GFP successfully colonizes maize’s roots and leaves endophytically. Subsequently, we evaluated whether RZ2MS9 has a synergistic effect on plant growth promotion when co-inoculated with Azospirillum brasilense Ab-V5, a commercial inoculant for maize. The two strains combined enhanced maize’s roots and shoots dry weight by 50.8% and 79.6%, respectively, when compared to the non-inoculated control. In addition, we used co-inoculation experiments in glass chambers to analyze the plant’s Volatile Organic Compounds (VOCs) production during the maize-RZ2MS9 and maize-RZ2MS9-Ab-V5 interaction. We found that the single and co-inoculation altered maize’s VOCs emission profile, with an increase in the production of indoles in the co-inoculation. Collectively, these results increase our knowledge about the interaction between the tropical PGPR Bacillus sp. RZ2MS9 and maize, and provide a new possibility of combined application with the commercial inoculant A. brasilense Ab-V5.ImportanceBacillus sp. RZ2MS9 is a PGPR, previously isolated from guarana plants cultivated in the Brazilian Amazon, which successfully promotes the growth of maize and soybean plants. To improve our knowledge about the interaction between this very promising PGPR and maize, we labelled RZ2MS9 with gfp and monitored it’s maize colonization. The transformation did not affect either RZ2MS9 growth nor its ability to promote maize growth in vitro. We demonstrated that RZ2MS9 colonizes endophytically maize’s roots and leaves. We also verified that the co-inoculation of RZ2MS9 and Azospirillum brasilense Ab-V5, a known commercial maize inoculant enhanced maize’s roots and shoots growth. Moreover, the co-inoculation altered the maize’s volatile organic compounds, increasing the production of indoles, that is related with decreased upon the reduction of fertilization. Certainly, our research contributed with better Bacillus sp. RZ2MS9 – maize interaction understanding and also provided new information concerning RZ2MS9 activity when applied with A. brasilense Ab-V5.