ObjectivesTo examine the effect of Nystatin oral rinse on oralCandida speciesandStreptococcus mutanscarriage.Materials and methodsTwenty healthy adults with oral candidiasis participated in the single-arm clinical trial and received Nystatin oral rinse for 7 days, 4 applications/day, and 600,000 International Units/application. Demographic-socioeconomic-oral-medical conditions were obtained. Salivary and plaqueCandida speciesandStreptococcus mutanswere assessed at baseline and 1-week and 3-month follow-ups. Twenty-four salivary cytokines were assessed.Candida albicansisolates underwent Nystatin susceptibility test.ResultsHalf of participants (10/20) were free of salivaryC. albicansafter using Nystatin rinse. SalivaryS. mutanswas significantly reduced at 3-month follow-up (p< 0.05). Periodontal status reflected by bleeding-on-probing was significantly improved at 1-week and 3-month follow-ups (p< 0.05). Plaque accumulation was significantly reduced at 1-week follow-up (p< 0.05). Interestingly, the responses to Nystatin oral rinse were not associated with race, gender, age, oral hygiene practice, adherence to Nystatin rinse, or sweet consumption (p> 0.05). NoC. albicansisolates were resistant to Nystatin. Furthermore, salivary cytokine eotaxin and fractalkine were significantly reduced at 3-month follow-up among participants who responded to Nystatin rinse (p< 0.05).ConclusionsThe study results indicate that oral antifungal treatment had an effect onS. mutanssalivary carriage. Future clinical trials are warranted to comprehensively assess the impact of antifungal treatment on the oral flora other thanS. mutansandCandida.Clinical relevanceDue to the potential cariogenic role of oralCandidaspecies, antifungal approaches shed new light on the prevention and management of dental caries from a fungal perspective.Supplementary informationThe online version contains supplementary material available at 10.1007/s00784-023-04969-5.