ω-3 Fatty acids have numerous health benefits, but their addition to foods is limited by oxidative rancidity. Spray-drying tuna oil-in-water emulsion droplets with a coating of lecithin and chitosan multilayer system could produce emulsion droplet interfacial membranes that are cationic and thick, both factors that can help control lipid oxidation. Physicochemical and oxidative stability of the spray-dried emulsions were determined as a function of storage temperature and relative humidity (RH). The combination of ethylenediaminetetraacetic acid (EDTA) and mixed tocopherols was able to increase the oxidative stability of dried emulsions. Lipid oxidation was more rapid during storage at low relative humidity (11% and 33% compared to 52% RH). At high moisture, physical modifications in the sample were observed, including reduced dispersibility and formation of brown pigments. Sugar crystallization or Maillard products produced at the higher humidities may have inhibited oxidation. Overall, spray-dried tuna oil-in-water emulsions stabilized by lecithin−chitosan membranes were more oxidatively stable than bulk oils and thus have excellent potential as an ω-3 fatty acid ingredient for functional foods.