The course of protein–lipid co‐oxidation was investigated in oil‐in‐water emulsions stabilized with proteins extracted from microwave‐treated (MWT) and conventional thermal‐treated (CTT) faba beans stored at 37°C for 7 days. Emulsions prepared with proteins from untreated (UT) faba beans and soy protein isolate (SP) were monitored for comparison. Lipid oxidation was detected through formation of primary and secondary oxidation products while protein oxidation was examined via tryptophan fluorescence degradation in interface and aqueous phase. Oxidation of proteins was more emphasized in the interfacial layers of MWT, CTT, and SP emulsions than in UT emulsions due to the prominence of radical chain‐driven co‐oxidation mechanism while lipoxygenase (LOX) activity in UT and MWT emulsions resulted in high amounts of hydroperoxides and abundance in lipid oxidation volatiles. Conventional thermal treatment provided better oxidative stability than microwave treatment reflected in lower levels of hydroperoxides and relative lack of diversity in lipid volatiles. Among detected volatiles, formation of ketones was more distinguished in MWT, CTT, and SP emulsions while UT emulsions contained a more diverse range of alkenals and alkanals. Ketones are known to form mainly through radical recombination reactions which combined with the results of protein oxidation supports that radical transfer reactions between proteins and lipids were the driving force behind oxidation in MWT, CTT, and SP emulsions. Treatments of faba beans resulted in increased oxidative stability of emulsified lipids and lower degradation of aqueous phase proteins.