Vegetable oils and their functional derivatives are considered good alternatives to replace petroleum-derived products due to their low toxicity, renewability, and biodegradable properties. Due to the high viscosity of vegetable oils, the current practice is to transesterify them into fatty acid methyl esters (FAMEs) to decrease reaction mixture viscosity. The use of FAME instead of vegetable oils towards the reactivity of functionalization can have an efect. To better understand the correlation between the reactivity and structure of vegetable oils, the comparison between the epoxidation of cottonseed oil (CSO) and their corresponding fatty acid methyl ester (CSO-FAME) was carried out in this study via percarboxylic acids, produced in situ. A frst comparison between the reactivity of performic and perpropionic acids was investigated. The efects of reaction temperature, HP/PA ratio, and catalyst loading on the epoxidation of CSO and CSO-FAME were evaluated. Important analytical work was done by using FTIR, NMR, GPC, and titrations to track the reaction extent and the nature of ring-opening products. The results show that CSO-FAME has a faster reaction rate both in epoxidation and ring-opening reactions. The use of perpropionic acid decreases the side reaction of ring-opening. The kinetics of CSO epoxidation was found to be faster than CSO-FAME.