A study of the microencapsulation process of omega-3 rich oil extracted from chia (Salvia hispanica L.) seeds was carried out, which included a comparative analysis of the microcapsules obtained by the spray- and freeze-drying methods using isolated soy proteins and maltodextrin as wall materials at different proportions. Color characterization of the obtained powders was performed and revealed a darker and yellower appearance of the freeze-dried samples compared with the spray-dried ones. Moisture content was measured for each sample and all presented values around 3.5%. The SEM micrographs revealed that spray-dried microcapsules can occur individually or may form clusters or aggregates, with the particles exhibiting a size range varying from 4 to 10 μm. Encapsulation efficiency was measured, with no significant differences found between drying methods or on varying the proportion of wall components (all samples presented values of approximately 60%). The oxidative stability of microencapsulated oils under accelerated oxidative conditions revealed protection factors 2-fold higher for all samples. In addition, microencapsulated oil stored under 25 °C revealed lower hydroperoxide values than those of unencapsulated oil throughout the whole storage test. Finally, oil encapsulated in SPI microcapsules also showed lower HPV values than that of the acceptable limit for virgin and cold-pressed vegetable oils (15 meq. O2/kg oil) during the storage test, while unencapsulated oil attained the acceptable limit in 62 days. This result represents an increase in the time of the oil shelf life of between 30 and 48%.