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Cowpea (Vigna sinensis L. var. Carilla) flours obtained by fermentation with inoculum Lactobacillus plantarum (PF) or with the natural microorganisms present in the flour (NF) and subsequent heat treatment in an autoclave were prepared to study the effect of fermentation on the antioxidant vitamin content and on the antioxidant capacity. Bacterial counts and pH values, vitamins C and E, carotenoids, glutathione (GSH), superoxide dismutase-like activity (SOD-like activity), peroxyl radical-trapping capacity (PRTC), lipid peroxidation in unilamillar liposomes, and Trolox equivalent antioxidant capacity (TEAC) were evaluated in raw and processed cowpea flours. gamma-Tocopherol and delta-tocopherol were found in raw cowpea, whereas vitamin C and carotenoids were not detected. An increase in the vitamin E activity was observed in PF, whereas vitamin C and carotenoids were not detected in fermented cowpea flours. Fermentation or heat treatment in an autoclave after fermentation produced processed cowpea flours with lower PRTC, glutathione content, and SOD-like activity than those of the raw seeds. However, those processes increased the capacity to inhibit the lipid peroxidation in unilamellar lipoposomes and TEAC. According to the results obtained in this study, the fermentation of cowpeas (naturally or with L. plantarum) and fermentation and subsequent heat treatment in an autoclave are good processes to obtain functional cowpea flours having higher antioxidant capacity than the raw legume.