Background Denture-related stomatitis is a common condition among denture wearers, primarily caused by Candida species, particularly Candida albicans. Traditional treatment methods, such as improved denture hygiene and antifungal medications, often fail to provide long term relief due to the recurrent nature of fungal colonization. This study aimed to evaluate the effectiveness of antifungal dental composites in managing Candida-associated denture stomatitis by assessing both clinical outcomes and microbiological changes over a three month period. Methodology This study was conducted at Women Dental College from April 2023 to April 2024, involving 93 participants diagnosed with Candida-associated denture stomatitis. Clinical severity was categorized using Newton’s classification, and baseline Candida colony forming unit (CFU) counts were recorded. Participants were randomly divided into two groups: one received antifungal-modified dental composites, while the control group received conventional composite applications. Follow-up assessments were conducted at one week, one month, and three months, evaluating clinical improvement and microbial reduction using standardized methods. Results Significant clinical improvement was observed in the experimental group, with recovery rates increasing from 55.9% at one week to 87.1% at three months. Microbiological analysis showed a steady decline in Candida CFU counts, decreasing from 7.9×10³ CFU/mL at baseline to 0.4×10³ CFU/mL after three months. The antifungal composite demonstrated sustained efficacy, reducing fungal colonization and promoting oral mucosal healing. Minimal adverse effects were reported, further supporting the safety of this approach. Conclusion The application of antifungal dental composites proved to be an effective intervention in managing Candida-associated denture stomatitis by providing continuous antifungal activity and reducing the need for repeated antifungal treatments. This method offers a promising non-invasive and long-term solution for denture wearers prone to fungal infections. Future studies should explore the long-term durability, mechanical properties, and broader clinical applications of these modified materials.