Major limiting factors of wide consumption of cowpea in day today diet include poor digestibility and the presence of anti-nutritional factors. Whole and dehulled seeds of eight improved cowpea lines grown in N’Djamena and Bebedjia (Chad) were analysed for four antinutritional factors contents (total phenols, tannins, flavonoids, phytates) and antioxidant activity, in order to assess the variability and the effect of decortication. In each locality, the experimental design was a triplicated randomly complete block design. Standard methods were used to evaluate these biochemical traits. The results showed a wide variability among genotypes for these traits in whole and dehulled seeds. In average, the decortication reduced polyphenols, tannins, flavonoids and phytate contents by 72.3%, 64%, 48.6% and 30.1% respectively. The dehulling also reduced the antioxidant activity by 42.25%. Dehulling appeared as a proper processing method to reduce anti-nutritional factors and improve the bioavailability of nutrients, especially when cowpeas are used as food for infants and children.