Background: Chickpea (Cicer arietinum L.), a self-pollinating legume being cultivated globally as a rich source of vegetarian protein. It plays an important role in human feed and nutritional security, especially in agricultural-based communities. Chickpea has higher bioavailability of protein, good sources of polyphenols and flavonoids. Besides their nutritional value, chickpea seeds contain various phenolic compounds. Phenolic compounds are of particular interest due to their contribution to the seed colour, sensory characteristics and several biological properties. Flavonoids are one of the main groups of phenolic compounds found in grain legumes. Desi and Kabuli chickpeas are being used worldwide and there are few studies where both desi and kabuli chickpeas seed flour for above properties with respect to physiological traits has been reported. Methods: The present investigation has been formulated to compare popular chickpea genotypes of desi and kabuli types for biochemical parameters viz., protein content, amino acid, total flavonoid content, total phenolic contents and RSA as well as two physiological traits i.e., chlorophyll content and leaf area index. The experiment consisted of 44 genotypes () grown in Randomized Block Design with row to row distance of 30 cm, in two replications during Rabi 2018-19. Result: The average crude protein content in desi and kabuli chana varied from 18.2% (Dollar variety) to 26.7% (JG315) and total phenolic content (TPC) ranged 1.22 to 0.74 mg/g. Total Flavonoid content (TFC) varied from 0.39 (ICCV-2) to 0.61 mg/g (JAKI-9218) with mean value of 0.47. Radical scavenging activity (RSA) in chickpea genotypes ranged from 36.2 to 49.5% with mean value of 40.86%. Total amino acid significantly correlated with TPC and TFC and TPC significantly correlated with TFC at 5% significant level.