The impact of typical primary or secondary lipid oxidation (LPO) products, selected as linoleic acid 13-hydroperoxide (13-HPODE) and malondialdehyde (MDA), on the structural modification of unadsorbed or adsorbed proteins in whey protein isolate (WPI)-stabilized oil-in-water (O/W) emulsions during storage up to 48 h at 37 °C in the dark was investigated. The results showed that either 13-HPODE and MDA could lead to structural modifications of unadsorbed or adsorbed proteins with a concentration-dependent manner and time relationship, respectively. Moreover, higher levels of MDA rendered a higher degree of oxidative modifications of WPI than 13-HPODE, indicated by the higher protein carbonyl contents and N’-formyl-L-kynurenine (NFK) and lower fluorescence intensity. Additionally, adsorbed proteins were more easily oxidized by LPO products than unadsorbed proteins. Overall, our results indicated that the formation of secondary LPO products and the protein position were crucial factors to increase the degree of oxidative modifications of WPI in O/W emulsion systems.