B. amyloliquefaciens PGPBacCA1 inhibited endophytic and soil-borne fungi of common beans. Surfactins, iturins and fengycins were responsible for the fungi antagonism. Lipopeptides lethally injured key structures of Sclerotinia and Fusarium strains. Bacilli cells did not affect the potential germination of either type of bean. Common bean seeds cv. Alubia and cv. Nag 12 were protected by PGPBacCA1.