Objective To evaluate the role of the biocontrol agent Bacillus subtilis CtpxS2-1 in inducing lupin systemic resistance against anthracnose caused by Colletotrichum acutatum by lipopeptide production. Results First, growth inhibition and thin layer chromatography-bioautography analysis confirmed that CtpxS2-1 cultures and their lipopeptide extracts, specifically fengycin, have strong antifungal activity against C. acutatum. Subsequent microscopic examination of these fungal inhibition zones showed mycelial pathogen deformations. PCR amplification of CtpxS2-1 confirmed the presence of genes encoding fengycins E and C, bacillomycin C, iturin A, and surfactins B and C. Based on this evidence, the effect of CtpxS2-1 and its lipopeptides on the induction of the lupin defence- and growth-related genes PR-1, PR-4, SOD-2, PIN-1 and PIN-3 was evaluated by RT-qPCR. In seedlings from roots treated with CtxpS2-1, a significant increase in the expression of these genes was induced. Efficacy assays showed that CtpxS2-1 treatment completely controlled anthracnose incidence (0.0%) compared with the untreated control. Furthermore, root and shoot growth in treated seedlings with CtpxS2-1 significantly increased due to disease control, as did the synthesis of the defence enzymes catalase, peroxidase and superoxide dismutase. Conclusion B. subtilis CtpxS2-1 is a key factor enhancing Andean lupin health by producing lipopeptides that damage C. acutatum cellular structures and inhibit their growth, as well as by inducing the expression of defence-related genes of lupin plants involved in systemic acquired resistance (SAR) against anthracnose.