This study aimed to optimize bean flours fermentation through the use of appropriate technological procedure and, thereby, to obtain a high quality and safe product. In this line, cowpea bean flours with different moisture conditions (10, 20 and 30%) were incubated with (1) a single culture of Lactobacillus plantarum, or (2) a consortium of lactic acid and acetic acid bacteria, together with one strain of Saccharomyces cerevisiae. Effects of inoculation of cowpea beans flours on stability (i.e., evaluated by the decrease in pH), and variations in nutritional characteristics (i.e., protein, starch, water soluble carbohydrates, total dietary fibre) were investigated. In both fermented flours, the effect of fermentation was more noticeable in total water-soluble carbohydrate (WSC) concentration during the fermentation process (P < 0.001), accounted for by metabolic activity of the microorganisms. The pH values progressively decreased (P < 0.001) through the fermentation process, particularly in flours fermented with a single culture of L. plantarum. By contrast, titratable acidity increased (P < 0.001) throughout the fermentation process in F2 and F3, although more noticeable in F3. Total dietary fibre (TDF) was not variable over the time. In relation to the protein content, the fermentations behaved very similarly; F2 had a variation over the time, but the effect was not significant (P = 0.0690). Results revealed small changes in chemical composition except in the case of pH and sugar contents with the values lower in the fermented products (i.e., single- or mixed-culture fermentation), leading to a more stable and safety product. These results indicate that fermented dry beans flours have the potential as functional ingredients for new food formulations.