Secondary metabolites have gained extensive research interest due to numerous commercial applications. However, these functional compounds are sensitive to adverse environmental and gastrointestinal conditions, impairing their use in food matrices and industrial applications. Nanotechnology has emerged as an important field in food industry which deals with rising customer concerns, expectations for natural, nutritious, and healthful industrial production of food items. Micro- and nanoencapsulation of natural compounds serve as a suitable technique to improve solubility, stability, and bioavailability of secondary metabolites. The present chapter summarizes significance of plant pigments as secondary metabolites and their applications, factors affecting their stability, and the reasons for poor bioavailability. Furthermore, insights are provided on various technologies (chemical, physicochemical, and physicomechanical) for encapsulation of plant pigments highlighting eco-friendly methods and classification of nanoencapsulation methods into groups (polymer, lipidic, and metallic). In particular, the effects of these encapsulation techniques on the stability, bioavailability, and bioactivity studies both in vitro and in vivo are reviewed in detail, providing scientific insights to gain resistance against adverse conditions. Additionally, to improve the influence of encapsulation on the production of valuable plant pigments, future directions and strategies for developing new formulations are discussed.