Postharvest decay in fruits and vegetables caused by fungal pathogens such as Botrytis cinerea leads to substantial economic losses. The decay caused by B. cinerea can be mitigated through the application of synthetic chemicals. However, due to its toxic residual effects on human health and environment stimulated the researchers to explore alternate effective and safe methods for the postharvest B. cinerea disease management. This article explains the current understanding of B. cinerea pathogenesis and the identification of antagonists used in the management of postharvest B. cinerea decay. This article also explains the mechanism of postharvest biocontrol agents (BCAs) and bioactive compounds derived from microorganisms and other plant resources with a particular focus on current advancements in molecular genomics such as (genetic engineering, transgenes and RNAi technology), omics and nanotechnology. Moreover, encapsulation of BCAs with nanoparticles increases their efficiency by delivering the BCAs to a specific host in a controlled and effective manner, with the aim of combating B. cinerea. Advanced molecular genetics allows for the identification and characterization of genes responsible for producing antifungal compounds produced by BCAs, which can be used to engineer strains with increased production of these compounds, making them more effective in controlling fungal diseases. Similarly, crops can be modified genetically which can show more resistance against the B. cinerea. However, more research will be needed to find the novel antimicrobial compounds derived from BCAs and estimation of developing beneficial microbial consortia for postharvest disease management, as well as genetic approaches, such as the use of CRISPR/Cas9 technology.