Beneficial effects of polyunsaturated fatty acids on health have generated increasing efforts for their incorporation into diet. Nevertheless, their high susceptibility to oxidative degradation have promoted the development of encapsulation technologies. Chia seed oil is known as a rich natural source of omega-3 and omega-6 fatty acids. In this work, essential fatty acids obtained by enzymatic hydrolysis of chia seed oil were encapsulated by inclusion complexation with amylose under the alkaline method. The effect of crystallization temperature (50, 70 and 90 °C) on the physicochemical properties of the samples was studied. The formation of amylose V-form was confirmed by X-ray diffraction. The C18:3 and 18:2 content of samples determined by gas chromatography was in the range of 2.4 – 3.0%. Peak melting temperatures determined by DSC were higher than 86 °C, showing an increase as the temperature of crystallization was increased. Results obtained by thermogravimetric analysis have shown that free fatty acids exhibited a mass gain associated to oxygen uptake, while it was not observed for amylose-lipid complexes, thus suggesting a protective effect of polyunsaturated fatty acids from oxidative deterioration. According to these results, amylose-lipid complexes would represent a promising delivery system for the incorporation of essential fatty acids into foods.