This study examines the in vitro antifungal properties and in vivo efficacy of thymol-cinnamaldehyde (TH-CIN) loaded nanocapsules, prepared using chitosan (CH) and hydroxypropyl methylcellulose (H) with varying ultrasonic power (200-600 W), for controlling Rhizopus stolonifer in papaya. Ultrasonic power notably influenced the nanocapsules' antifungal properties, both in vitro and in vivo. Higher ultrasonic power resulted in improved antifungal activity, with NC-CH-400 and NC-CH-H-600 formulations achieving the highest inhibition zones (94.67 % and 93.33 %, respectively) against R. stolonifer in vitro. The Minimum Inhibitory Concentration (MIC) for CH formulations was 6.25 mg/mL, while the Minimum Fungicidal Concentration (MFC) for all formulations was 50 mg/mL. Protein leakage assays demonstrated significant disruption of R. stolonifer cell membranes, with NC-CH-400 and NC-CH-H-600 at MFC reducing intracellular protein concentrations by over 95 %. In vivo tests showed that NC-CH-400 nanocapsule-coated papayas, whether sprayed or dipped, reduced weight loss to 0.54 % and 0.86 %, respectively, and exhibited lower decay severity indices, particularly during storage. Spraying was more effective than dipping in preventing decay. Peel color analysis revealed that coated fruits maintained acceptable ripeness levels over 10 days, indicating delayed maturation. Coated fruits also exhibited better color consistency and were preferred in sensory evaluations for improved taste, aroma, color, and texture, particularly with NC-CH-400 and NC-CH-H-600 coatings.