The effects of air classification and lactic acid bacteria fermentation on the reduction of anti-nutritional factors (vicine and convicine, trypsin inhibitor activity, condensed tannins and phytic acid) and in vitro protein and starch digestibility of faba bean flour were studied. Free amino acid (FM) profile analysis was also carried out. Air classification allowed the separation of the flour into protein and starch rich fractions, showing different chemical compositions and microstructures. Lactobacillus plantarum growth and acidification in faba bean flour and its fractions were assessed. The anti-nutritional compounds were separated mostly to the fine protein-rich fraction. Fermentation caused the decrease of vicine and convicine contents by more than 91% and significantly reduced trypsin inhibitor activity and condensed tannins (by more than 40% in the protein-rich fraction). No significant (P > 0.05) variation was observed for total phenols and phytic acid content. Fermentation increased the amount of FAA, especially of the essential amino acids and gamma-aminobutyric acid, enhanced the in vitro protein digestibility and significantly lowered the hydrolysis index. This work showed that the combination of air classification and fermentation improved nutritional functionality of faba bean flour which could be utilized in various food applications.