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Bacillus species are among the most studied and commercially exploited biocontrol agents of plant‐parasitic nematodes. These antagonists may control nematodes by producing toxic or repellent substances, inducing systemic resistance in plants and disrupting nematode chemotaxis. Understanding the mechanism of action of antagonists increases the likelihood of success for microbiological nematicides under field conditions. Therefore, the objective of this work was to elucidate the mechanisms of action of Bacillus amyloliquefaciens strain BaNCT02 against Meloidogyne incognita. We assessed the potential of this strain for forming biofilm in roots and producing volatile and non‐volatile toxic substances. BaNCT02 did not induce systemic resistance in tomato plants against M. incognita. Scanning electron microscopy and chemotaxis analyses revealed that the bacteria form a biofilm on soybean roots and 67% of second‐stage juveniles of M. incognita are repelled by common bean roots treated with the antagonist. Additionally, BaNCT02 produces substances with toxic effects against eggs and juveniles of M. incognita, including volatile organic compounds such as 2‐undecanone and 2‐heptanone, as well as non‐volatile metabolites like proteases and chitinases. The suppressive effect of these substances on hatching and mortality of juveniles varied from approximately 70% to more than 90%. We concluded that B. amyloliquefaciens BaNCT02 forms a biofilm on root surfaces and produces volatile and non‐volatile metabolites with nematicidal and repellent effects against M. incognita. [ABSTRACT FROM AUTHOR]