Increased research interest in the health benefits of fish oils and the wide publicity of these studies have led to the marketing and launch of a wide array of new and traditional food and beverage products enriched with omega-3 fatty acids. This chapter focuses on the impact of microencapsulation and other factors on the bioavailability of omega-3 fatty acids from fish oils. To help understand the impact of microencapsulation on bioavailability of omega-3 fatty acids, it presents a brief overview of encapsulation techniques and excipients used. Microencapsulation of fish oil improves its chemical stability by preventing oxidation and ensuring satisfactory organoleptic properties. Even though encapsulation excipients food matrices and lipid structures can affect the absorption rate of omega-3 fatty acids in short-term studies, microencapsulated fish oil and omega-3 fatty acids enriched foods are equally efficient for providing these essential fatty acids as fish oil in long-term applications.