Dragon fruit (Selenicereus spp.) is a high‐value crop in the Philippines. It is commonly propagated using stem cuttings, which quality is essential for fruit production. Several pathogens have been reported to cause various diseases in dragon fruit worldwide. These diseases affect stem and fruit quality in the field, but the consequences during storage are unknown. This study aims to determine the effect of three pathogens (Neoscytalidium dimidiatum, Epicoccum sorghinum, and Nigrospora sphaerica) on Selenicereus stem cuttings in controlled storage conditions. Three weeks after inoculation, only N. dimidiatum significantly reduced Selenicereus stem weight in both cooler (air‐conditioned storage area/19‐25°C) and warmer (room temperature/28‐30°C) temperatures. Nonetheless, all pathogens induced symptoms on stems, which caused a loss in product quality. Neoscytalidium dimidiatum caused significantly more severe symptoms under controlled conditions. In general, symptoms were more severe on the stems kept in the air‐conditioned storage area. This study highlights the importance of disease‐free planting materials and adequate temperature in the storage area in the preparation and dissemination of high‐quality dragon fruit stem cuttings.