The use of chemical preservatives for fruit preservation raises concerns regarding food safety and microbial resistance, while non-thermal physical antimicrobial technology, though eco-friendly, often demonstrates limited efficacy. This study investigated a hurdle antifungal approach combining indirect plasma processed air (IPPA) and peracetic acid (PAA) using Chinese bayberries as a model fruit, aiming to reduce PAA dosage without compromising antifungal efficacy. The results show that the hurdle treatment (0.1% PAA + IPPA) achieved comparable antifungal efficacy to 0.5% PAA alone, reducing native fungal colonies by 1.63 log10 CFU/g (vs. 1.57 log10 CFU/g) and inoculated Penicillium citrinum colonies by 1.67 log10 CFU/g (vs. 1.77 log10 CFU/g). Moreover, the PAA-IPPA hurdle treatment could reduce the weight loss rate, delay the decrease in firmness, and increase the antioxidant enzyme activities of Chinese bayberries. Overall, the PAA-IPPA hurdle treatment efficiently inhibits microbial growth, enhances fruit antioxidant capacity, and partially replaces the need for chemical preservatives.