The study of bulk nanobubbles (NBs) has long been an interest of the scientific community. Recent studies have highlighted the revolutionary role of NBs as nanoscale engineers in the synthesis of functional nanomaterials in a sustainable, controllable and soft-template manner. In this process, the preparation and stability control of NBs is particularly critical, which directly determines the performance of the soft template and the quality and functionality of the final material. This review focuses on the key breakthroughs of NBs as green and soft templates for the fabrication of functional nanomaterials. The emerging technique, which allows for the control over the size, morphology, and properties of the nanomaterials by adjusting the characteristics of the bulk NBs templates, shows significant promise. The burgeoning preparation techniques for NBs, including physical and chemical methods, are first outlined. The application scenarios and relative merits of different NBs producing methods are compared and analyzed. Recent advances in the control of NBs stability are then discussed, considering the influence of temperature, pH, surfactant, electrolyte, and gas properties on NBs stability. Finally, the recent achievements of NBs-templated nanomaterials for the applications in uranium extraction, catalysis and desalination are emphasized, while the underlying mechanisms for material preparation and optimization are also discussed.