Denture stomatitis affects around 50% of denture wearers in certain populations as a prevalent oral mucosal lesion. There has been a high interest in utilizing natural antibacterial composites, such as medicinal plants extracts. Punica granatum, a popular medicinal plant, has various pharmacological applications. In this particular research, iron NPs were formulated by the Punica granatum aqueous extract, following the principles of green chemistry. The study objective was to assess the effectiveness of FeNPs on denture stomatitis. The usual analytical examinations were applied for FeNPs. The FE-SEM results confirmed that the nanoparticles exhibited a spherical morphology, with sizes ranging from 21.6 to 65.8 nm. This clinical trial involved 30 patients who received FeNPs. Over a period of two weeks, the patients were instructed to consume the mouthwash four times per day, with 15–20 drops each time, for a duration of 2–3 minutes. Following the mouthwash, they were advised to refrain from eating or drinking for 0.5 hour. The patients in both classes were instructed to consume the medication at particular times. The erythema and inflammation levels were recorded and assessed at each session using a 6-point scale and a graded blade. Additionally, palatal mucosa mycological samples were collected for culture during each visit. The data revealed a notable reduction in the palatal erythema surface compared to the initial condition in the follow-up visits. This study suggests that FeNPs can effectively reduce the Candida colonies number and the area affected by erythema in the denture stomatitis management.