The impact of temperature, emulsifier, and protein type on the reactivity of malondialdehyde in oil-in-water emulsions was elucidated. Malondialdehyde recoveries in aqueous buffer, protein solutions, saturated oil, and fully hydrogenated coconut oil-in-water emulsions stabilized by whey proteins or Tween 20 at 4 or 40 °C were compared. At both temperatures, the reactivity of malondialdehyde in aqueous buffer was the same. In protein solutions, malondialdehyde concentrations were reduced further and its decrease was protein-dependent. Similar trends were found for emulsions. Surprisingly, malondialdehyde was very reactive in saturated oil because only 15% was recovered at 40 °C. However, the degradation in oil proved to be strongly temperature-dependent; at 4 °C, losses amounted to only 8%. This study revealed that malondialdehyde is a very reactive molecule, both in the presence and absence of proteins. Its use as a general oxidation marker should therefore be considered with care.