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The microencapsulation technology consists of a trap of a compound inside a tiny sphere known as microsphere. The microencapsulation concerns many different active materials such as bioactive compounds, drugs, vitamins, enzymes, flavors, and pesticides. This technology has gained real interest in numerous fields such as agriculture, cosmetic, pharmaceutical, textile, and food. This chapter highlights the encapsulation of essential oils into nanoemulsion-based delivery system as a model for the encapsulation of natural bioactive compounds. Moreover, an investigation of different parameters affecting the stability of produced nanoemulsion was conducted, in addition to the study of the effect of the nanoencapsulation of essential oils on their antibacterial activity. Finally, an enumeration of the advantages of encapsulating essential oils into nanoemulsion-based delivery systems in order to provide a natural food preservatives has been provided.