Nanotechnology research within food and agriculture systems in Indonesia has been increasing. However, these nanotechnology studies remain narrowly focused on source exploration, isolation, characterization, and potential use and not enough on sustainability and safety aspects. Indonesia's small- and medium-scale enterprises have also commercialized nanoproducts for fertilizer, herbal medicine, and food supplements in limited volumes. These enterprises are affiliated with the Agency for the Assessment and Application of Technology Indonesia (BPPT)/National Research and Innovation Agency (BRIN) and/or universities through research-business incubation programs with government support. While the Government of Indonesia's masterplans and standards have mainstreamed nanotechnology, the key deliverables are primarily publications, patents, and intellectual property rights, giving little direction toward applying nanotechnology for commercial purposes (i.e., industrial products). Policies and legislation are yet to be enacted to regulate nanotechnology, although nanoproducts are already being commercialized. The challenges to applying nanotechnology in Indonesia's agrifood systems include high cost, difficulties in fabrication and characterization, low investment in research and development, lack of advanced technologies, and limited information on nanoproduct toxicology, safety, and risks. In addition, the safety (toxicity and risks) and sustainability of nanotechnology need further systematic study and guidance.