This study aimed to evaluate the impact of genotypes and tannin levels on the nutritional characteristics of faba bean seeds and their relation to protein molecular structure profiles using Fourier transform infrared spectroscopy (FTIR). Eight genotypes with low tannin (LT, n = 3) and normal tannin (NT, n = 5) levels were studied. Standard methods of analysis and NRC 2001 were used to obtain chemical and energy parameters. The protein molecular spectral study was performed using a spectrometer JASCO FT/IR–4200. Molecular features were analyzed in the mid-infrared region at ∼4000–800 cm⁻¹ and protein-related functional groups were obtained using OMNIC software. Results showed higher (P < 0.01) soluble crude protein (SCP), rapidly degradable protein fraction (PA2), and intestinal digestibility of bypass protein (dIDP) in LT than NT. The slowly degradable protein fraction (PB2) was higher in NT (P < 0.01) compared to LT. Higher absorbance was observed in spectral peaks related to amide I, amide II, and β-sheet in NT (P < 0.05) compared to LT. The area ratio of amide I to amide II and the height ratio of α-helix to β-sheet were higher in LT compared to NT (P < 0.01). This study provides a better understanding of associations between structure and nutritional characteristics in faba bean genotypes with different tannin levels.