Nanobubbles, with diameters typically ranging from about 1 to 200 nm, have attracted growing attention from food and agricultural researchers in recent years owing to distinctive properties such as an exceptionally high specific surface area, prolonged persistence in the liquid phase, capacity to generate reactive oxidizing species, and ability to penetrate complex microstructures. In this paper, the definition, types, and physicochemical properties of nanobubbles are first introduced, followed by the main production methods, along with the advantages and limitations of each. The paper then discusses applications of nanobubbles across various areas of the food industry, including dairy processing, enhancement of probiotic survival, protection of bioactive compounds, food freezing, washing and sanitization of fresh produce, water treatment and reclamation, and removal of microbial biofilms and pesticide residues, as well as agricultural applications, particularly in drip and subsurface irrigation systems. Despite this promising evidence, the technology faces significant challenges, including the lack of standardized production and characterization methods, the difficulty of isolating the independent effect of nanobubbles from co-occurring factors (such as gas type and the mechanical energy of the generation process), the absence of industrial-scale cost–benefit studies, and unresolved consumer-safety concerns. Based on the findings of this paper, conducting pilot-scale studies, designing controlled experiments to disentangle the underlying mechanisms, and developing standardized guidelines are essential to enable the safe and effective deployment of this emerging technology across the food supply chain.