This study examines how consumers perceive agricultural products affected by natural disasters, using apples in Japan as a case study. Typhoons and other natural disasters frequently damage the surface of apples during the production season, causing significant harm to farmers’ businesses, particularly when a large typhoon hits the production area. To maintain the sustainability of agricultural production, consumers need to purchase damaged crops at a certain price. To assess the effect of product attributes, such as appearance and price, and personal attributes of respondents, we conducted a choice-based conjoint analysis using a mixed logit model. The estimated results using the main effect and cross-section models show that consumers generally devalue apples when they have scratches. However, by using consumer co-operatives on a daily basis and disseminating simple information about the relationship between scratches and natural disasters, we could mitigate this devaluation tendency and thus contribute to sustainable agricultural production.