Fruit and vegetables are an important part of human diets and provide multiple health benefits. However, due to the short shelf-life of fresh and minimally-processed fruit and vegetables, significant losses occur throughout the food distribution chain. Shelf-life extension requires preserving both the quality and safety of food products. The quality of fruit and vegetables, either fresh or fresh-cut, depends on many factors and can be determined by analytical or sensory evaluation methods. Among the various technologies used to maintain the quality and increase shelf-life of fresh and minimally-processed fruit and vegetables, biological control is a promising approach. Biological control refers to postharvest control of pathogens using microbial cultures. With respect to application of biological control for increasing the shelf-life of food, the term biopreservation is favored, although the approach is identical. The methods for screening and development of biocontrol agents differ greatly according to their intended application, but the efficacy of all current approaches following scale-up to commercial conditions is recognized as insufficient. The combination of biological and physical methods to maintain quality has the potential to overcome the limitations of current approaches. This review compares biocontrol and biopreservation approaches, alone and in combination with physical methods. The recent increase in the use of meta-omics approaches and other innovative technologies, has led to the emergence of new strategies to increase the shelf-life of fruit and vegetables, which are also discussed herein.