Catalytic oxidation of sustainable raw materials like unsaturated fats and oils, or fatty acids and their esters, lead to biobased, high-value products. Starting from technical grade methyl oleate, hydrogen peroxide as a green oxidant produces only water as by-product. A commercially available, cheap water-soluble tungsten catalyst is combined with Aliquat® 336 as a phase-transfer agent in solvent-free reaction conditions. In this study, we first report the transfer of this well-known batch system into continuous mode. The space–time yield is improved from 0.08 kg/L.h in batch to 1.29 kg/L.h in flow mode. The improved mass transfer and reduced back mixing of the biphasic liquid–liquid slug flow allows for selectivity control depending on physical parameters of slug flow namely volumetric phase ratio, volumetric flow rate, and slug length. Even though the product, methyl 9,10-epoxystearate is obtained at a maximum selectivity of only 58% in flow mode, higher space time yield combined with possible reactant recycling in flow mode offers a promising avenue of research. This work analyses the use of slug flow parameters as tools for controlling selectivity towards oxidation products of methyl oleate.