Fish has been a potential food source for humans. Labeo bata is a commonly consumed fresh water fish species, particularly in South India. This study explored the effect of different cooking (boiling, steaming, microwaving, and frying) on structural, morphology, nutritional profile, and in-vitro antioxidant activity of Labeo bata. All these processing methods reduced the water content and improved the quantity of major nutrients. Foremost changes were obtained in the FT-IR spectra of processed fillets with respect to the intensity and shifting of major bands in specific regions. Amino acids, fatty acid profile and mineral content values were also varied significantly (P<0.05) upon processing. Physico-chemical characteristics including cooking loss, water activity, color, and pH of both raw and cooked Indian mackerel differed significantly (P<0.05). In-vitro antioxidant activity was analyzed using the QUENCHER procedure. The DPPH and ABTS scavenging capacity of cooked fillets ranged from 14.8 to 28.0 and from 19.3 to 34.5 mmol Trolox Eq./kg.fish dry basis, respectively.