Apple production holds a prominent position in Morocco’s Rosaceae family. However, annual production can fluctuate due to substantial losses caused by fungal diseases affecting stored apples. Our findings emphasize that the pre-storage treatment of apples, disinfection of storage facilities, box type, and fruit sorting are pivotal factors affecting apple losses during storage. Additionally, the adopted preservation technique was significantly correlated with the percentage of damage caused by fungal infections. Blue mold accounts for nearly three-quarters of the diseases detected, followed by gray rot with a relatively significant incidence. This study has revealed several fungal diseases affecting stored apples caused by pathogens such as Penicillium expansum, Botrytis cinerea, Alternaria alternata, Trichothecium roseum, Fusarium avenaceum, Cadophora malorum, and Neofabraea vagabunda. Notably, these last two fungal species have been reported for the first time in Morocco as pathogens of stored apples. These data affirm that the high losses of apples in Morocco, attributed primarily to P. expansum and B. cinerea, pose a significant threat in terms of reduced production and diminished fruit quality. Hence, adopting controlled atmosphere storage chambers and implementing good practices before apple storage is crucial.