Fruit are susceptible to quality loss and deterioration after harvest due to high metabolic and physiological activities. Over the last four decades various postharvest treatments have ensured maintenance of quality, control of diseases or decay by slowing down the postharvest ripening and senesce. The fruit quality change during postharvest however, has been mostly explored using physicochemical characteristics. Considering the complexity of fruit physiology and metabolism, the application of omics techniques could aid the in-depth analysis and understanding of fruit quality change during postharvest treatment. Therefore, this review presents recent information on the application of integrated omics (transcriptomics, proteomics, and metabolomics) in postharvest research, with an overview on fruit quality and safety. Trends in omics data analysis for fruit during postharvest handling was highlighted. The role of integrated omics in improving our understanding of fruit response during natural postharvest progression (towards decay) during storage, as well as in case of induced responses due to the application of biocontrols was discussed. The article concluded with the outlooks of future studies on the application of integrated omics as the catalyst for innovative postharvest solutions.