In the prospect of use of natural products as safe and eco-friendly alternatives to chemical pesticides, the Bacillus nakamurai BDI-IS1 strain, derived from a Burundian soil sample, was selected among other bacterial isolates for its in vitro strong antimicrobial activities against a range of bacterial and fungal phytopathogens. Genome mining coupled with metabolomics revealed that it produces bioactive secondary metabolites including surfactins, iturins A, bacillaenes, bacillibactin, bacilysin, plantazolicin, and potentially amylocyclicin, bacinapeptin and LCI. The antagonistic activity of some of these metabolites was demonstrated by testing mutant strains of BDI-IS1. Although this bacterium is not able to produce the large arsenal of secondary metabolites as the commercial strain Bacillus velezensis QST713, greenhouse experiments show that BDI-IS1 is able to protect tomato and maize plants against early blight and northern leaf blight caused by Alternaria solani and Exserohilum turcicum, respectively, at levels similar to or better than QST713. The reduction of these foliar diseases, following root or leaf application of the bacterial suspension demonstrates that BDI-IS1 can act by direct antibiosis and by inducing plant defence mechanisms. These findings indicate that B. nakamurai BDI-IS1 can be considered as a good candidate for biocontrol of plant diseases prevailing in tropical regions, and encourage further research into its spectrum of activity, its requirements and the conditions needed to ensure its efficacy.