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The fumigation of apples using methyl bromide (MeBr) can cause severe deterioration in fruit quality. Moreover, maintaining the quality of apples during postharvest storage and eradicating pests, especially those involved in quarantine issues, are important for facilitating the export of apples, including the “Fuji” apple (<i>Malus pumila</i> var. “Fuji”) in South Korea. In the present study, phosphine (PH₃) fumigation as an alternative to MeBr was found to be more effective for the control of peach fruit moth larvae (<i>Carposina sasakii</i>), which had naturally infested Fuji apples, at a high temperature (25 °C) rather than at a low temperature (5 °C). To achieve the industry requirement of better-quality perishable commodities and meet quarantine guidelines for export, PH₃ fumigation at the low temperature (5 °C) was followed by cold treatments at 3 ± 2 °C for 2 and 4 weeks, which led to higher efficacy than was achieved using PH₃ at 5 °C alone. Given that chemical treatments, such as treatment with 1-methylcyclopropene, can inhibit ethylene synthesis, low-temperature PH₃ fumigation for 72 h followed by 4 weeks of cold treatment could also extend the shelf life of apples and resolve known quarantine issues when used as an alternative to MeBr treatment.