There has been an emerging trend for consumers to pursue nutritional and healthier food. To achieve this goal, food industries have been seeking methods to incorporate bioactive compounds into food matrices; however, this has been a challenging task since some of those compounds have off-flavors, off-colors, or they are susceptible to oxygen, light, heat, water, and many other processing conditions, which further limits their applications. Furthermore, it is also important to consider how to maintain the structure of those compounds intact during oral consumption, gastric, and intestinal tract digestion, as these components are expected to have structural transformation and lose their health benefits. This dissertation aims to find solutions to enrich food products with bioactive compounds while maintaining their functionality, stability, and bioavailability, ensuring minimal impact on the organoleptic properties of the final products. Microencapsulation is one of the promising techniques in which subjecting the bioactive compounds into the homogeneous or heterogeneous matrix offers opportunities for custom designed for the proper protection of each specific compound. Chapter 1 introduced background knowledge about currently applied techniques and challenges in encapsulating bioactive compounds, as well as challenges in incorporating those compounds into food products. Chapter 2 showed the encapsulation of acetylcysteine (NAC) through spray drying and air drying, and the obtained samples' morphology, release profile, as well as encapsulation efficiency, were investigated. To expand NAC’s application as a nutraceutical supplement, chapter 3 discussed the encapsulated NAC within a semi-solid water-in-oil high internal phase emulsion (HIPE) and successfully maintained its taste and stability. Chapter 4 displayed the method of applying thickening and gelling hydrocolloids to strengthen the HIPEs internal structures. Gastrointestinal digestion was also discussed in the chapter. Chapter 5 showed another direction of bioactive compound’s application, which includes forming inclusion complex as clean label stabilizers in Pickering emulsions to give the final product tunable amphiphilicity and ultrastability. This research provides insights into the encapsulation of bioactive compounds through versatile platforms to mask the off-flavor, enhance the physiochemical properties, improve bioavailability, and expand the applications of bioactive compounds. Chapter 6 summarized the key findings of the research and Chapter 7 showed the fabrication drawbacks and future aspects regarding formulation modification to expand the applications of the obtained products. This research provides insights into the encapsulation of bioactive compounds through versatile platforms to mask the off-flavor, enhance the physiochemical properties, improve bioavailability, and expand the applications of bioactive compounds.