Due to strong clinical data supporting a variety of health benefits, omega-3 oils are being increasingly added to food and beverage products. However, these bioactive lipids need to be protected against autoxidation and degradation during food processing and storage. Microencapsulation technology is employed to stabilise omega-3 oils and enable their delivery into food and beverage products without impacting the taste and shelf-life of the product. In this chapter, we provide an overview of microencapsulation techniques used to encapsulate and stabilise omega-3 oils. The advantages and disadvantages of each method are described and compared. Also, important properties of the microencapsulated ingredients, such as payload, oxidative stability and bioavailability, are described. Although a variety of methods have been used to microencapsulate omega-3 oils, two methods are primarily used commercially. These are complex co-acervation and spray-dried emulsion formation. These two methods are compared and contrasted, and their future development discussed.