Over the last three decades, decontamination management of fresh fruits and vegetables (FFVs) in the packhouses and along the supply chains has been heavily dependent on chemical‐based wash. This has resulted in the emergence of resistant foodborne pathogens and often the deposition of disinfectant byproducts on FFVs, rendering them unacceptable to consumers. The management of foodborne pathogens, microbial contaminants, and quality of FFVs are a major concern for the horticultural industries and public health. Activated water systems (AWS), such as electrolyzed water, plasma‐activated water, and micro–nano bubbles, have gained significant attention from researchers over the last decade due to their nonthermal and nontoxic mode of action for microbial inactivation and preservation of FFVs quality. The aim of this review is to provide a comprehensive summary of recent progress on the application of AWS and their effects on quality attributes and microbial safety of FFVs. An overview of the different types of AWS and their properties is provided. Furthermore, the review highlights the chemistry behind generation of reactive species and the impact of AWS on the quality attributes of FFVs and on the inactivation/reduction of spoilage and pathogenic microbes (in vivo or in vitro). The mechanisms of action of microorganism inactivation are discussed. Finally, this work highlights challenges and limitations for commercialization and safety and regulation issues of AWS. The synergistic prospect on combining AWS for maximum microorganism inactivation effectiveness is also considered. AWS offers a potential alternative as nonchemical interventions to maintain quality attributes, inactivate spoilage and pathogenic microorganisms, and extend the shelf‐life for FFVs.