Bitter rot is a disease of apple caused by fungi in the genus Colletotrichum. Management begins with removal of infected twigs and fruit from tree canopies to reduce overwintering inoculum. Infected apple fruit are usually tossed to the orchard floor, which is generally managed as herbicide-treated weed-free tree rows, separated by grass drive rows. We monitored decay rates and succession of fungi of apple fruit with bitter rot in tree canopies, and on the soil surface in tree rows, grass drive rows, and nearby diverse plant communities. We hypothesized that decay would occur most rapidly within diverse plant communities, which would provide a more diverse array of potential fungal decomposers. Apple fruit in tree canopies became dry and mummified and had more Colletotrichum gene marker copies the following growing season than did fruit on the soil surface. Of the soil-surface samples, those in grass drive rows and diverse plant communities had higher moisture, faster decay rates, and sharper decreases in Colletotrichum gene marker copies than apple fruit in tree rows. Fungal composition across all decaying apple fruit was dominated by yeasts, with higher genus-level richness, diversity, and evenness in fruit from tree canopies than those on the soil surface. In soil-surface apple fruit, we observed clear successional waves of Pichia, Kregervanrija, and [Candida] yeasts, with similar but distinctly diverging fungal composition. Our results show that orchard floor management can influence fungal succession in apple fruit with bitter rot but suggests that bitter rot management should primarily focus on removing infected apple fruit from tree canopies.