Managing post-harvest decays in citrus fruit without relying on conventional pesticides presents a significant challenge in modern Plant Pathology. This study aimed to evaluate the efficacy of the biological control agentCandida oleophilastrain O in controlling green mold caused byPenicillium digitatumthroughout various stages of the post-harvest supply chain. Using a series ofin vivoexperiments, different scenarios ofP. digitatuminfections in clementine tangerine, orange, and lemon fruit were examined, with treatments applied before, during or after infection. The study simulated typical conditions of the citrus supply chain, including picking, processing in packinghouses, and transportation, as well as cold storage and shelf-life phases. Results indicated thatC. oleophilaexhibited significant efficacy in reducing green mold symptoms, even at shelf-life temperatures, making it a practical alternative to conventional fungicides. Additionally, the study provided insights into the molecular mechanisms underlying the defensive response of citrus fruit toC. oleophilatreatment, with up-regulation of defense-related genes observed across different fruit types. Overall, this study underscores the potential ofC. oleophilaas a sustainable and effective solution for managing post-harvest decays in citrus fruit within the complexities of the supply chain.