Vegetable oils are renewable biomass that can substitute fossil raw materials for sustainable development. These oils are made of different types of fatty acids (building blocks), which could lead to differing reactivity toward chemical reaction. In order to investigate the correlation between reactivity and structure of vegetable oils, we have compared the reactivity of epoxidized cottonseed oil (ECSO) and its epoxidized fatty acid methyl ester (EFAME) toward carbonation reaction by using the homogeneous catalyst tetrabutylammonium bromide (TBABr). Mass transfer and physicochemical properties were determined and further applied to estimate the intrinsic rate constants during the kinetic modeling stage. It was found that densities for both systems were similar, but the difference in viscosity was important. Mass transfer coefficients were similar for the carbonated species, but the ones of EFAME and FAME were found to be ca. 100 times lower than those of ECSO and CSO. The solubility of CO2 was found to be higher in FAME derivatives than in CSO derivatives. We have found that the rate constant of carbonation of EFAME can be 1.4 times higher than the one of ECSO. A linear relationship between the carbonation rate constant of epoxidized vegetable oil and its fatty acid methyl ester with temperature was found.