Nectarines can be affected by many diseases, resulting in significant production losses. Natural products, such as essential oils (EOs), are promising alternatives to pesticides to control storage rots. This work aimed to test the efficacy of biofumigation with EOs in the control of nectarine postharvest diseases while also evaluating the effect on the quality parameters (firmness, total soluble solids, and titratable acidity) and on the fruit fungal microbiome. Basil, fennel, lemon, oregano, and thyme EOs were first tested in vitro at 0.1, 0.5, and 1.0% concentrations to evaluate their inhibition activity against Monilinia fructicola. Subsequently, an in vivo screening trial was performed by treating nectarines inoculated with M. fructicola, with the five EOs at 2.0% concentration by biofumigation, performed using slow-release diffusers placed inside the storage cabinets. Fennel, lemon, and basil EOs were the most effective after storage and were selected to be tested in efficacy trials using naturally infected nectarines. After 28 days of storage, all treatments showed a significant rot reduction compared to the untreated control. Additionally, no evident phytotoxic effects were observed on the treated fruits. EO vapors did not affect the overall quality of the fruits but showed a positive effect in reducing firmness loss. Metabarcoding analysis showed a significant impact of tissue, treatment, and sampling time on the fruit microbiome composition. Treatments were able to reduce the abundance of Monilinia spp., but basil EO favored a significant increase in Penicillium spp. Moreover, the abundance of other fungal genera was found to be modified.

White haze, an emerging disorder caused by extensive fungal growth on the apple surface, results in a compromised fruit quality and decreased marketability. The use of biological control agents could be an interesting tool to reduce its development. This work aimed to test the efficacy of two Aureobasidium pullulans strains (AP2 and PL5) in controlling white haze on stored apples. An in vivo trial was conducted by inoculating fruits with white haze causal agents (Entyloma belangeri, Golubevia pallescens, Tilletiopsis washingtonensis) and treating them with the antagonistic yeasts. Three commercial biofungicides were also included in the trial. Both A. pullulans strains, along with the Metschnikowia fructicola-based product, reduced white haze incidence after 110 days of storage at 1 ± 1 °C and after 7 days of shelf life. Furthermore, the effect of A. pullulans application on the fruit fungal microbiome was assessed. A significant impact of apple matrix and treatment on the mycobiome composition was observed. Analyses showed a good colonization of A. pullulans on the treated apples, both epiphytically and endophytically. A decrease in white haze-related fungi abundance was observed in the treated fruits. Additionally, a reduction of Ramularia spp. and modifications in the abundance of other fungal genera were detected after storage and shelf life.