Over a third of fresh produce worldwide is lost postharvest before it reaches consumers, and one of the main threats contributing to this is decay by postharvest pathogens. Postharvest fungicides are commonly used to control for these pathogens, but increasing concerns about fungicide resistance and environmental impacts create a pressing need for additional methods as a supplement or replacement. One important area of exploration is the microbiome, which has the potential to protect the host from pathogens as competitors to and antagonists of pathogens. Therefore, it is important to understand how fruit microbiomes assemble based on ecological factors and how treatments aimed at fruit physiology shift those microbiomes. This work focused on how apple postharvest microbiome is shaped by these factors. Low oxygen storage, inhibiting ethylene biosynthesis with aminoethoxyglycine to limit ripening, the antioxidant scald inhibitor diphenylamine, and waxing in a commercial packing line were found to shift the microbiome. In addition, genetically engineered apples with reduced sorbitol biosynthesis harbored distinct microbiomes, as well as apples in the lower canopy that likely received more dispersal from soil. Overall, this work shows how postharvest apple microbiomes are connected to core aspects of fruit physiology and microbial ecology, highlighting their complexity and potential usefulness in future integrated approaches to control postharvest pathogens and promote greater food security.