Chia oil has a high content of linolenic and linoleic acids, which are essential for the human body. However, their high degree of unsaturation (double bonds) makes the oil very susceptible to oxidation. In this context, the use of spray drying can be useful strategy to minimize the oxidation of this oil. Thus, the aim was to assess the effects of inlet temperature and feed rate conditions involved in the spray drying process on the physicochemical and morphological characteristics, and stability of the chia oil microparticles with maltodextrin and GA. The microparticles were obtained with a yield of 50%, encapsulation efficiency greater than 87%, low‐moisture content, and mean particle sizes ranging from 3.01 to 4.11 μm. The thermal evaluation and storage evidenced an increase in stability. The 1H HR‐MAS NMR technique showed that the microparticles maintained the characteristic fatty acid profile of chia oil and seeds. Results indicate that the microencapsulation methodology was suitable for preparing microparticles containing chia oil.