Microbial spoilage in commercial apple storage facilities can lead to Food Loss of up to 30% during the storage period. Here we aimed to characterize the microbiome and the abundance of pathogens on the apple skin and to elucidate the influence of the apple variety, orchard management practices and the dynamics of the microbial composition during the entire storage period. The results allow for description of infection levels of different pathogens at harvest and the prediction of post-storage symptom development. Additionally, information about the community composition allows for identification of the main factors driving the composition of the microbiome, the change in diversity during the storage period and the identification of beneficial microorganisms that may eventually be applied as biocontrol agents. The results can be applied in the development and improvement of infection models, inform breeders on how the host genotype interacts with the microbial community and inform researches on how microbial communities assemble over time.