Microencapsulation of ω-3 fatty acids by spray drying was studied using both monolayered (lecithin) and multilayered (lecithin-chitosan) fish oil emulsions with maltodextrin as wall material. Stability of the multilayered emulsions was higher than the monolayered ones, and increased with the increase of the concentration of chitosan. No differences were detected in the moisture or MY of the microcapsules related to the different composition of the corresponding emulsions. On the contrary, MEE was significant higher in the case of the microcapsules produced with the multilayered emulsions with the highest concentration of chitosan (1 % w/w), being related with lower detection of TBARS at high storage temperatures. Overall, this study shows the suitability of microencapsulating ω-3 fatty acids by spray drying using both monolayered and multilayered fish oil emulsions with maltodextrin as wall material. Multilayered microcapsules prepared with lecithin-chitosan emulsions provide a great protective effect against lipid oxidation of fish oil during storage at moderate to high temperatures (30 °C and 60 °C). These multilayered microcapsules could be therefore successfully used as a fish oil protection approach for storage before its use as an ingredient in food products.