Virgin coconut oil (VCO) is produced by processing the flesh of coconut (Cocos nucifera L.). It has beneficial health effects due to the medium-chain fatty acids (MCFA), vitamins, and antioxidant contents. Since liquid VCO is not widely accepted by consumers for direct consumption, further processing into powder VCO can be achieved using microencapsulation methods, such as single-layer emulsification (SL), layer-by-layer emulsification (LBL), and complex coacervation (CC). Therefore, the present work aimed to determine the characteristics of microencapsulation of VCO powder by emulsification and coacervation complex methods over 30 days of storage period. Results showed that SL VCO emulsion remained stable for three days of storage, while LBL VCO emulsion experienced syneresis. The particle size of the reconstituted VCO powder was also larger than the fresh emulsion. LBL microcapsule had the highest yield at 74.17%, and there was an increase in moisture content (MC) during 30 days of storage in CC microcapsule. Meanwhile, MC of SL microcapsule was constant, and the equilibrium MC of LBL was retained during 15 days of storage. A microencapsulation efficiency of up to 78.65% was obtained for CC, and the value decreased for all microcapsules during the 30 days of storage. Different oxidative characteristics were also reported, resulting in increased peroxide value of VCO powder. Furthermore, all microcapsules had amorphous and glassy surface morphology, as well as different characteristics and stability during storage.