Ethanolic extracts of propolis and bee honey contain substances beneficial to human health. Mixtures of wall materials were compared in spray-drying microencapsulation of ethanolic extracts of propolis and bee honey rich in bioactive compounds. Maltodextrin and tara gum were used to obtain microencapsulates A, and modified native potato starch and tara gum were used for microencapsulates B. High values of phenolic compounds, flavonoids, and antioxidant capacity were obtained in microcapsules A and B, and the results obtained in terms of encapsulation efficiency, yield, hygroscopicity, solubility, moisture, Aw, bulk density, and color were typical of the spray-drying process. On the other hand, spherical and elliptical microparticles of sizes between 7.83 and 53.7 µm with light and medium stability were observed. Thermogravimetric properties were similar in both microencapsulates; total organic carbon, SEM-EDS, and FTIR analyses corroborated the encapsulation. X-ray diffractogram exhibited amorphous structures, and the release kinetics of phenolic compounds presented high values from 8.13 to 12.58 mg GAE/g between 7 and 13 h. Finally, modified potato starch is a better encapsulant than maltodextrin because it has better core protection and controlled release of the encapsulated bioactive compounds.