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The human oral cavity is colonized by a diversity of microorganisms living harmoniously. When an imbalance occurs in this population, also called dysbiosis, opportunistic microorganisms lead to oral infections. Nystatin, a traditional antifungal, and red propolis, a resinous mixture collected by honeybees from plant source, can be used to control oral infections. Using β-cyclodextrin (βCD) inclusion complexes with nystatin and red propolis may improve the solubility, stability and antimicrobial activity of these substances, making it possible to include these complexes in pharmaceutical formulations. This study aimed to obtain these inclusion complexes by solubilization and characterize and evaluate their antimicrobial activity against microorganisms from the oral cavity. The inclusion complexes showed loss of crystallinity and the infrared spectra showed interactions between the substances. The content of total polyphenol ranged from 4.32-4.62 mg/g, while the content of flavonoids was between 3.05-3.83 mg/g. The red propolis (Prop):βCD(1:1 and 2:1) complexes were the most active against S.aureus, S.epidermidis, S.mutans and C.albicans with Minimum Inhibitory Concentration (MIC) ranging between 32-256 µg/mL. The inclusion complex of nystatin (Nys):βCD(1:1) effectively inhibited C.albicans growth (MIC=4µg/mL). Interestingly, the association between Nys:βCD(1:1) and Prop:βCD(1:1 or 2:1) showed a synergic effect, improving antifungal activity when compared to red propolis complex alone.