Background <p>Bacterial endophytes are a rich source for the bioprospection of chemical compounds with biological activities for application as bio-fungicides. The potential fungicidal activity of secondary metabolites from <i>Bacillus</i> MHSD_36 was evaluated in vitro and in silico against <i>Botrytis cinerea</i>.</p> Results <p>The secondary metabolites showed both spore germination and mycelial growth inhibition against <i>B. cinerea</i>. In silico analysis confirmed the presence of gene clusters involved in the synthesis of secondary metabolites, from terpenes, beta-lactams and nonribosomal peptides classes, with antimicrobial activity. Liquid chromatography-mass spectrometry putatively identified secondary metabolites mainly composed of metabolites from the terpenoids and oligopeptide classes. Furthermore, molecular docking analysis revealed that the identified secondary metabolites exhibited a strong binding affinity towards <i>B. cinerea</i> pathogenicity factors, including aspartic protease, cutinase, lipase, and pectin methyltransferase. The strongest binding affinity (-6.644&#xa0;kcal/mol) was observed towards aspartic protease, which was greater than the highest binding affinity (-4.783&#xa0;kcal/mol) with a commercially used synthetic fungicide, captan. The annotated metabolites had a low predicted acute toxicity.</p> Conclusion <p>Therefore, secondary metabolites from <i>Bacillus</i> MHSD_36 are composed of compounds with potential fungicidal activity against <i>B. cinerea</i>.</p>