Some strains of Bacillus vallismortis have been reported to be efficient biocontrol agents against tomato pathogens. The aim of our study was to assess the biocontrol ability of the endophytic strain BL01 Bacillus vallismortis through in vitro and field trials, as well as to verify its plant colonization ability and analyze the bacterial genome in order to find genes responsible for the biocontrol activity. We demonstrated in a gnotobiotic system and by confocal laser microscopy that the endophytic strain BL01 was able to colonize the endosphere and rhizosphere of tomato, winter wheat and oilseed rape. In vitro experiments demonstrated the inhibition activity of BL01 against a wide range of phytopathogenic fungi and bacteria. BL01 showed biological efficacy in two-year field experiments with tomato plants against black bacterial spotting by 40–70.8% and against late blight by 47.1% and increased tomato harvest by 24.9% or 10.9 tons per hectare compared to the control. Genome analysis revealed the presence of genes that are responsible for the synthesis of biologically active secondary metabolites, which could be responsible for the biocontrol action. Strain BL01 B. vallismortis can be considered an effective biocontrol agent to control both fungal and bacterial diseases in tomato plants.