The influence sodium alginate (SA) as an outer layer agent on bioaccessibility and matrix food release of purified chia oil (PCO) microencapsulated was investigated. PCO microparticles with Capsul were elaborated and optimized by response surface methodology (RSM), and then as an encapsulating agent and SA as an outer layer (PCO-Capsul/SA) were designed by mini spray-drying with 2 fluid nozzle (2-N) and 3 fluid nozzle (3-N). The optimal conditions obtained for PCO-Capsul system were: dryer inlet temperature of 114 °C and PCO:Capsul relation of 1:5.42. After the addition of SA out layer, PCO-Capsul/SA microparticles were subjected to in vitro static gastrointestinal digestion. PCO-Capsul/SA occurred mainly in the intestinal phase, showing the suitability of SA as an intestine-site release polymer. However, when PCO-Capsul/SA was incorporated into a yoghurt (Y), microparticles showed a significantly lower PCO matrix food release and bioaccessibility after in vitro digestion than PCO-Capsul-Y microparticles, due to their interaction between SA and Y. SA spray-dried by 3-N showed great potential for vehiculation of omega-3 rich oils in the future incorporation and develop of functional foods.