The effective management of stored fruits is a critical issue, and new strategies for the control of postharvest fungal diseases are urgently required. The current global market requires long-term storage capabilities to ensure the availability of fruits and vegetables all year round to a large number of consumers. Due to the wide variety of crops, different environmental conditions are necessary to guarantee quality and safety of stored products. The main cause of product losses is estimated to be microbial. Cold storage represents a crucial phase for the control of postharvest pathogens because of the lack of effective fungicides and active ingredients allowed. Generally, postharvest management was based on synthetic products, but this strategy caused the emergence of resistant strains. Moreover, issues related to chemical residues in the fruit have recently made these treatments challenging to justify, and this has stimulated the exploration of alternative strategies. The European Union is also pushing to accelerate the transition to a more sustainable food system with the “European Green Deal”. Microorganisms, together with physical treatments, basic substances, and plant extracts, could represent sustainable alternative methods to synthetic pesticides. Actually, only one commercial product based on a yeast is approved in the EU for postharvest disease management. Nevertheless, it is necessary to develop new complementary strategies to counteract postharvest pathogens and, at the same time, to guarantee food safety and security.