Insect-mediated pollination increases yields of many crop species and some evidence suggests that it also influences crop quality. However, the mechanistic linkages between insect-mediated pollination and crop quality are poorly known. In this study, we explored how different pollination treatments affected fruit set, dry matter content (DMC), mineral content and storability of apples. Apple flowers supplementary pollinated with compatible pollen resulted in higher initial fruit set rates, higher fruit DMC and a tendency for lower fruit K:Ca ratio than flowers that received natural or no pollination. These variables are related to desirable quality aspects, since higher DMC is connected to higher consumer preference and lower K:Ca ratio is related to lower incidence of postharvest disorders during storage. Using structural equation modelling, we showed an indirect effect of pollination treatment on storability, however mediated by complex interactions between fruit set, fruit weight and K:Ca ratio. The concentrations of several elements in apples (K, Zn, Mg) were affected by the interaction between pollination treatment and apple weight, indicating that pollination affects element allocation into fruits. In conclusion, our study shows that pollination and the availability of compatible pollen needs to be considered in the management of orchard systems, not only to increase fruit set, but also to increase the quality and potentially the storability of apples.