Aflatoxin B1 (AFB1) and ochratoxin A (OTA) are among the most important mycotoxins with common presence in bread and bakery products. Biological detoxification of mould food spoilage and mycotoxin contamination by lactic acid bacteria (LABs) exhibits high potential on a cost-effective and large scale. In this work, the effect of Lactobacillus strains isolated from goat milk whey on reducing AFB1 and OTA during bread making was evaluated by the determination of mycotoxin reduction potential of 12 LAB strains after 72 h incubation in De Man-Rogosa-Sharpe (MRS) broth (37 °C). The most effective LABs were lyophilized and added as ingredient in bread formulation, analysing mycotoxins by high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry after bread fermentation and baking. AFB1 was reduced in MRS broth by seven LABs (11-35%), highlighting Lactobacillus plantarum B3 activity; while all LABs reduced OTA (12-40%) with L. plantarum B3 and Lactobacillus paracasei B10 as the most active strains. Both LABs were lyophilized and added in contaminated bread with and without yeast, reaching AFB1 and OTA reductions up to 27% and 32% respectively in dough and up to 55% and 34% respectively in bread. The selected strains significantly reduced AFB1 and OTA during bread fermentation, pointing to a potential biocontrol strategy for mycotoxins detoxification in bread and bakery products. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.