Unsaturated fatty acid concentrates (UFAC) were nanoencapsulated by emulsification/lyophilization using chitosan:gelatin matrices as wall material. Nanoemulsions presented droplets size between 40 and 280 nm. There was a decrease in droplets size due to gelatin addition, resulting in a decrease of encapsulation efficiency and an increase in porosity and pores volume. UFAC oxidation in chitosan capsules was slower than in free oil. Sorption isotherms were performed at 4 and 25 °C, and GAB model showed the best fit to experimental data. Differential enthalpy and entropy increased with the moisture content decrease, and the adsorption process was spontaneous. Pores radius increased with the increase of gelatin in the microstructures. The critical storage conditions of the microstructures were calculated. The range of water activity, which represents the maximum stability zone, was of 0.65–0.75 at 4 °C and of 0.73–0.85 at 25 °C. This zone hinders the oxygen diffusion through the pores, retarding oxidation.
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