In this study the influence of fermented bean seed flour (BF) with Lactobacillus plantarum 299v on bioactive compounds, antioxidant activity and selected inhibitory activity of wheat wafers were investigated. Wheat wafers with addition of BF (10%, 20%, 30%, 40% and 50%), fermented bean flour wafers (100%) and wheat wafers (WF) were prepared. The results indicated that wafers made from 100% fermented bean seed flour were characterized by the highest content of bioactive compounds (0.086 mg mL−1 for proteins, 0.79 mg mL−1 for peptides, and 0.46 mg mL−1 for polyphenols), compared with the control sample. The highest peptide content after the hydrolysis process and DH were found for 100% BF (2.29 mg mL−1 and 32.81%, respectively). The antiradical activity against ABTS·+ was noted for hydrolysates obtained from 40% BF (IC50 = 17.81 μg mL-1) and against DPPH· in the case of hydrolysates from 30% BF (IC50 = 34.43 μg mL-1). In turn, 50% BF exhibited higher Fe2+ chelating activity than the control sample (IC50 = 4.57 μg mL-1). The IC50 values were the same for hydrolysates from wafers with 50% BF and 100% BF and 0.14, 0.24, and 0.19 mg mL−1 for α-glucosidase, lipase, and ACE respectively.