Background: Omega-3 fatty acids are essential fatty acids that the body cannot create itself; thus, they must be obtained from functional foods. Therefore, the food processing industries are becoming more interested in the production of omega-3 enriched food products, as consumers and healthcare organizations are increasingly demanding functional foods with minimal fatty acid loss and higher oxidative stability. Moreover, the stability of long-chain, polyunsaturated fatty acids in functional foods is a major challenge for the food processing industries. Therefore, the spray drying method was used to prepare spray-dried microcapsules (SDMs) with the minimum loss of, and more stable, fatty acids. Methods: In this study, emulsion blends of chia seed oil (CSO, 50%) and fish oil (FO, 50%) were spray-dried using varied operating conditions, including the inlet air temperature (IAT) (125, 140, 155, 170, and 185 °C), wall material (WM) (5, 10, 15, 20, and 25%), pump speed (PS) (3, 4, 5, 6, and 7 mL/min), and needle speed (NS) (3, 5, 7, 9, and 11 S). Results: The maximum loss of ALA in the spray-dried microcapsules (SDMs) was observed (9.90 ± 0.40%) at 170 °C, and the minimum loss was 4.18 ± 0.20% in run order 9. A similar trend was observed in the maximum retention loss of EPA and DHA (9.71 ± 0.39% and 9.77 ± 0.39%) at a high temperature of 170 °C, while the minimum losses of EPA and DHA were observed in run order 9. Furthermore, the maximum peroxide value (PV) of the SDMs was observed at a lower temperature of 140 °C (1.45 ± 0.19 meq O2/kg), and the minimum PV was 1.33 ± 0.16 meq O2/kg. Conclusions: Overall, based on the results, we concluded that the oxidative stability of the SDMs was improved and that it can be used as a fortifying agent in the processing of many food products.