The availability of different food products containing bioactive compounds promotes their inclusion in the daily diet of consumers. However, the effective and safe delivery of such products requires certain precautions to ensure their preservation, stability, and bioavailability when consumed. Microencapsulation is a great alternative, which is a method capable of protecting different bioactive compounds, including probiotic cells, prebiotic compounds, and some antioxidant substances such as phenolic compounds, anthocyanins, flavonoids, and vitamins. Therefore, this study aimed to perform a literature review and present different alternatives to make bioactive compounds viable through microencapsulation, increase their stability and viability when applied in different food matrices, and address the existing challenges regarding their effectiveness.