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The fungus <i>Macrophomina phaseolina</i> is the causal agent of charcoal rot in many crops, such as strawberries and beans. Symptoms include stem and root rot and chlorotic foliage. This disease’s management is complicated because the pathogen forms resistant microsclerotia. This work aimed to obtain bacterial isolates for the biocontrol of <i>M. phaseolina</i> in arid regions. Two strains that grew well under low pH and high salinity, named BsA3MX and BsC11MX, were isolated and identified as <i>B. amyloliquefaciens</i>, based on their morphology and analysis of the 16S ribosomal RNA. Both strains inhibited <i>M. phaseolina</i> up to 66.8% in vitro through the combined action of volatile and diffusible compounds. Furthermore, they produce siderophores and indole-3-acetic acid (IAA), have ACC-deaminase activity, solubilize phosphate and zinc, and decrease microsclerotia germination. Moreover, in greenhouse assays using cowpea plants (<i>Vigna unguiculata</i> L.), strain BsA3MX reduced lesions caused by <i>M. phaseolina</i> and induced a significant increase in foliage and root biomass. Overall, these results suggest <i>B. amyloliquefaciens</i> BsA3MX and BsC11MX can be used as biological control agents against <i>M. phaseolina</i> in arid zones.