BACKGROUND: Apples are among the most important horticultural crops. Therefore, maintaining their postharvest quality is essential. Storage diseases, such as Bull's Eye Rot (BER), which is caused by Neofabraea spp. (syn. Pezicula, Phlyctema), poses a significant economic challenge to apple production. Its suppression is particularly significant as compared to other posthar- vest pathogens due to a specific latent mode of action. This work aims to improve BER disease management and fruit microbial quality in apple production, both of which are key aspects of sustainable horticultural systems. RESULTS: In order to meet this objective, we propose a novel approach based on a sustainable biopreparation (named APPAT(f) REE), composed of spores of selected antagonistic strains, Bacillus velezensis strains B134/22, B233/22, B267/22, and Tricho- derma koningiopsis G779/22 as active ingredients, supplemented with targeted prebiotics (1% of D-xylose and D-ribose mix- ture). The biopreparation effect was evaluated under orchard conditions following cold storage to demonstrate its applicability in horticultural practice. A methodological approach facilitating the microbial community acquisition of apples was established using membrane filtration. The biopreparation was found to improve the microbial quality of apples by reduc- ing community metabolic stress and positively modulating the composition of fungal taxa in the apple mycobiome as com- pared with the chemical fungicide treatment. CONCLUSION: The APPAT(f)REE study demonstrates a multifaceted approach to Neofabraea spp., including support for the nat- ural apple fruit microbial communities, and thus it promotes a sustainable pest management system.