Our hypothesis tested the efficacy and safety of a mucoadhesive oral gel formulation of Brazilian propolis extract compared to miconazole oral gel for the treatment of denture stomatitis due to Candida spp. infection in older adults. Forty patients were randomly allocated in a noninferiority clinical trial into two groups. The control group (MIC) received 20 mg/g miconazole oral gel and the study group (PROP) received mucoadhesive formulation containing standardized extract of 2% (20 mg/g) propolis (EPP-AF®) during 14 days. Patients were examined on days 1, 7, and 14. The Newton's score was used to classify the severity of denture stomatitis. The colony forming unity count (CFU/mL) was quantified and identified (CHROMagar Candida®) before and after the treatment. Baseline characteristics did not differ between groups. Both treatments reduced Newton's score (P < 0.0001), indicating a clinical improvement of the symptoms of candidiasis with a clinical cure rate of 70%. The microbiological cure with significant reduction in fungal burden on T14 was 70% in the miconazole group and 25% in the EPP-AF group. The EPP-AF appears to be noninferior to miconazole considering the clinical cure rate and could be recommended as an alternative treatment in older patients.