Vitamins, peptides, essential oils, and probiotics are examples of health beneficial constituents, which are nevertheless heat‐sensitive and possess poor chemical stability. Various encapsulation methods have been applied to protect these constituents against thermal and chemical degradations. Encapsulates prepared by different methods and/or at different conditions exhibit different microstructures, which in turn differently influence the encapsulation efficiency as well as retention of encapsulated core materials. This review provides a summary of various microstructures resulted from the use of selected encapsulation methods or systems, namely, spray coating; co‐extrusion; emulsion‐, micelle‐, and liposome‐based; coacervation; and ionic gelation encapsulation, at different conditions. Subsequent effects of the different microstructures on encapsulation efficiency and retention of encapsulated core materials are mentioned and discussed. Encapsulates having compact microstructures resulted from the use of low‐surface tension and low‐viscosity encapsulants, high‐stability encapsulation systems, lower loads of core materials to total solids of encapsulants and appropriate solidification conditions have proved to exhibit higher encapsulation efficiencies and better retention of encapsulated core materials. Encapsulates with hollow, dent, shrunken microstructures or thinner walls resulted from inappropriate solidification conditions and higher loads of core materials, on the other hand, possess lower encapsulation efficiencies and protection capabilities. Encapsulates having crack, blow‐hole or porous microstructures resulted from the use of high‐viscosity encapsulants and inappropriate solidification conditions exhibit the lowest encapsulation efficiencies and poorest protection capabilities. Compact microstructures and structures formed between ionic biopolymers could be used to regulate the release of encapsulated cores.

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