Spray-drying is known as a common and economical technique for the encapsulation of various nutrients and bioactive compounds. However, shear and thermal tensions during atomization and dehydration, as well as physicochemical instability during storage, result in a loss of these compounds. As a solution, bioactives are stabilized into different carriers, among which proteins and peptides are of particular importance due to their functional properties, surface activity, and film/shell formability around particles. Given the importance of stabilization of bioactive compounds during spray drying, this paper focuses on the role of composition and type of carriers, as well as the characteristics and efficiency of various protein-based carriers in the encapsulation and maintaining of physicochemical, structural, and functional properties, along with biological activity of bioactive compounds (e.g., oleoresins, sterols, polyphenols, anthocyanins, carotenoids, probiotics, and peptides), and nutrients (e.g., vitamins, fatty acids and minerals) alone or in combination with other biopolymers.