The total antioxidant capacity (TAC) and total phenolic compounds (TPC) of cocoa beans and chocolate produced from spontaneous and inoculated fermentations of different cocoa varieties were evaluated. Fourier transform infrared spectroscopy (FTIR), as well as conventional methods: 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), was used to determine TAC and TPC. Chocolate showed higher (p<0.05) TPC (47.17–57.16mgGAE/g) and TAC (1.66–2.33mMTE/g and 8.86–11.35mMTE/g as measured by DPPH and ABTS, respectively) than cocoa beans (6.30–26.05mgGAE/g, 0.24–1.17mMTE/g and 1.29–4.83mMTE/g for TPC, DPPH and ABTS, respectively). Partial least square (PLS) model for infrared data showed a good calibration coefficient (R2cal>0.94), indicating that the FTIR technique represents a fast and reliable tool to evaluate TPC and TAC in cocoa beans and chocolate. Display omitted •Antioxidant capacity was evaluated in chocolate and cocoa beans from different variety.•Chocolates showed higher TPC and TAC than cocoa beans.•Chocolate produced by spontaneous fermentation of PH15 showed the lowest TPC and TAC.•Cocoa variety and yeast inoculation affect TPC and TAC of chocolate.•FTIR is a reliable tool to evaluate TPC and TAC in cocoa beans and chocolate.