In this work, pea flour and two milling fractions obtained by industrial-scale air classification were characterized and fermented by Lactiplantibacillus plantarum to increase their nutritional value. Scanning electron microscopy and chemical analysis revealed major differences in the morphology and composition of the flours. Protein-rich (43.7 %) fraction exhibits a few-fold higher mineral, spermidine (290 μg/g), but also a higher phytate (20.4 mg/g) content compared to starch-rich fraction. Flour type and inoculum majorly influenced the composition of the fermented product. In spontaneously fermented flours, biogenic amines accumulated up to 6.6 mg/g, which was the main drawback besides the large variations between batches, as confirmed by metagenomic analysis. Higher contents of lactic acid, free amino groups formed by proteolysis and gamma-aminobutyric acid were determined in inoculated fermentations of protein rich fraction, whereas a higher relative bioavailability of minerals was found in the inoculated starch-rich fraction, as the phytate content was reduced by 42 %.