Latent infections caused by Monilinia spp. in nectarines cause great economic losses since they are not detected and rejected at harvest and can appear at any time post-harvest, even at the consumer’s home. The effect of a pre-cooling chamber, water dump operation, and cold-storage chamber on the activation and/or development of preharvest latent infections caused by Monilinia spp. on nectarines were studied under different postharvest conditions: (a) cold storage for 0, 1, or 3 d at 4 °C at either 75% relative humidity (RH) or 100% RH before water dumping, (b) water dumping for 10 minutes at 15 °C, and (c) cold storage for 0, 3, or 10 d at 4 °C at either 75% RH or 100% RH after water dumping. These storage conditions were transformed to fungal physiological time. For visualization of the latent infections caused by Monilinia spp., the nectarines were placed in sterile paper bags and frozen at −20 °C for 48 h in order to damage the epidermis. To compare different handling scenarios, the incidence of latent infection was modelled for physiological time description by a modified Gompertz model. The activation and/or development of preharvest natural latent infections caused by Monilinia spp. at postharvest was mainly related to temperature and incubation time at postharvest. Storing nectarines with any postharvest handling less than 11 days at 4 °C avoids brown rot symptoms and reduced the activation and/or development of pre-harvest latent infections caused by Monilinia spp., while more cold days caused the exponential phase of latent infection activation and/or development. The Gompertz model employed could be used for predicting the activation and/or development of latent infection caused by Monilinia spp. at postharvest conditions and looks at the postharvest life. To our knowledge, this is the first time that the effects of post-harvest handling on latent infections in fruit have been studied.