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Cyclic lipopeptides (LPs) are potentially promising in the agricultural, industrial and pharmaceutical sectors. LPs have a variable hydrophilic cyclic peptide part attached to a variable fatty acid chain. One limitation of these compounds is their low availability due to their limited production by bacteria. The objective of this study was to identify and quantify homologues of LPs biosynthesized by Bacillus amyloliquefaciens using ultra-performance liquid chromatography (UPLC–MS/MS) after inducing the synthesis of these secondary metabolites using different inducers, including chemical compounds and inactive cells of Colletotrichum sp. Four homologues were identified in the iturin family (bacillomycin D), and the iturin homologue with the highest synthesis was the molecular ion m/z 1031.54, with 173.1 µg mg−1 crude extract. In addition, seven homologues were detected in the fengycin family (four of fengycin A and three of fengycin B), and the homologue with the highest content was the molecular ion m/z 1463.69 (fengycin A), with 3288 ± 528.5 ng mg−1 crude extract. Finally, five homologues were identified in the surfactin family, where the highest concentration was observed for the molecular ion m/z 1036.68, with 61.5 ± 3.01 µg mg−1 crude extract. The highest concentration of LP homologues (iturin, fengycin and surfactin) synthesized by B. amyloliquefaciens was detected in the presence of inactive cells of Coletotrichum sp., suggesting that the inducing substance is associated with the inducer’s cell envelope and could be a single protein or a structure that includes protein components.