Omega-3 fatty acids can be widely considered as potential therapeutic agents due to their antioxidant, nutritional, and health aspects. They have unsaturated nature which leads to susceptibility to oxidation conditions. Therefore, to get the maximum health benefit and to minimize or prevent the process of oxidation, omega-3 rich oils must be protected against atmospheric oxygen. To achieve this objective, two strategies were usually carried out: First addition of an antioxidant to the oils, and second, the encapsulation process. Here we review omega-3 fatty acids chemistry, natural sources, health benefits, and antimicrobial activity. This review highlights obstacles to incorporating omega-3 fatty acids in foods, particularly concerning oxidation. The importance of incorporating natural polyphenols especially curcumin as well as using different wall materials (sodium alginate, chitosan, and natural clays) in microencapsulating fish and flaxseed oils were also discussed. Different techniques of encapsulation were highlighted as well.