In this study, an efficient and high-yield simultaneous epoxidation and transesterification of fatty acid methyl esters in a single-pot reaction is presented. Starting from commercially available renewable unsaturated fatty acid methyl esters (FAMEs) from plant oils, the epoxidation catalyzed by Novozym 435 was optimized for a temperature of 50 °C in two different reactor types on the multigram scale. Simultaneous transesterification of the methyl esters to iso-nonyl esters was also studied and optimized for same conditions resulting in an efficient process for synthesis of epoxy fatty acids esters from renewable feedstock.