Lipid oxidation deteriorates the sensory and nutritional quality of food emulsions containing polyunsaturated fatty acids. Classically, different extraction solvents are used as a first step to measure lipid oxidation in emulsions. However, it is unclear how the applied extraction method influences the measured lipid oxidation values. In this work, we systematically examined the performance of common solvent mixtures such as chloroform, methanol, and hexane (or isooctane)–isopropanol on lipid extraction from emulsions stabilized with different emulsifiers (Tween 20 (T20), whey proteins, and pea proteins) and oxidation levels, and how this, in turn, affected the measured hydroperoxide concentrations. Chloroform–methanol was the most effective solvent (lipid yield >93 wt.%). When using hexane–isopropanol, extraction yields were consistently high for T20‐ and pea protein‐based emulsions (>60 wt.%), but in whey protein‐based emulsions, values as low as 26 wt.% were measured. In case of incomplete extraction, hydroperoxide concentrations measured by colorimetric methods need to be corrected for this effect. When using 1H NMR to assess lipid oxidation, the actual amount of extracted lipids is intrinsically taken into account. This highlights not only the importance of the extraction method in determining lipid oxidation in emulsions but also that of the actual analysis method.Practical application: This study highlights that the lipid extraction yield can vary depending not only on the emulsion composition (e.g., type of emulsifier) but also on the oxidative state of the emulsion and the extraction solvent used. If this is overlooked, errors can be made in the hydroperoxide determination. Although these effects can be corrected for, this is not standard procedure, which implies that awareness on this matter should be increased. It is also important to point out that depending on the solvent used, the different lipid classes (including various lipid oxidation products) may be extracted at different levels. Chloroform–methanol should be preferred for extraction of all lipid and lipid oxidation‐derived molecules, including aldehydes.