The demand for nutritional and functional food is increasing due to the change of consumer’s consumption pattern. With growing awareness of health concerns, consumer not only seek for foods that are delicious, but also those that are highly nutritious and functional. However, multiple challenges are associated with active nutritious ingredients, including their low solubility, inappropriate physical state, low physicochemical stability, low biochemical stability, poor flavor profile, and poor handling characteristics. Microencapsulation can be a good technique to solve such problems, as it can provide capabilities to protect, control release, and modify the properties and texture of active ingredients. Typically, a good microencapsulation system requires capabilities for economic production, compatibility with target food matrix, high protection toward destabilizing environments, high encapsulation efficiency, increased bioavailability, and delivers ingredients with desired mechanism in a controlled release manner. Furthermore, additional microencapsulation functions are needed in the food industry, e.g., retard chemical degradation, mask undesirable flavors, prevent flavor loss, provide antimicrobial activities, and modify food textures. In addition to delivering nutritious food cargos, consumers also seek for food that are made from ingredients with smaller environmental footprints. Specifically, sustainable methods and materials to form microcapsules are in high demand. However, current encapsulation methodology focuses on chemical ingredient modification, which is time-consuming with large environmental drawbacks and is difficult to scale up. Thus, we aim to investigate facile sustainable methods for the microencapsulation of unstable active ingredients to be used to solve food-related problems. Generally, active food ingredients that have been largely explored for encapsulation can be divided into two categories, hydrophobic and hydrophilic ingredients. Hydrophobic ingredients generally require encapsulation to prevent oxidation, avoid heat degradation, and improve bioavailability. Hydrophilic ingredients, such as natural colorants, vitamins and proteins are often pH-sensitive and unstable. To date, it is still challenging for researchers to develop suitable microencapsulation systems for specific components. Therefore, we provided a systematic investigation on microencapsulation methods featuring internal core structuring and surface shell modification, specifically, to encapsulate multiple model compounds for various applications in functional food and beverages. With our findings, microencapsulation is no longer an added-value technique, but a new solution to a broad array of food ingredient applications.