Application of nanotechnology in the agrifood system and the rising number of nanofood products on the market are creating concerns among consumers and other stakeholders. These concerns and other potential barriers to the commercialization of agrifood nanotechnology products may limit the ability to capture its full potential. Understanding the emerging trends and the links between underlying values, expressed attitudes, and actual behaviors involving consumer acceptance of agrifood nanotechnology is important for governance, risk regulation, and the achievement of the full potential of agrifood nanotechnology. The purpose of the study was to use systems mapping to examine and analyze critical links between consumer acceptance of agrifood nanotechnology and factors such as trust, stakeholders, institutions, knowledge, and human environmental health risks. The study used a meta-analysis of the risk perception literature and solicited the opinions of experts to develop the systems map. Factors affecting consumer acceptance of agrifood nanotechnology are dynamic, complex, interactive, and interdependent, and consumer decisions to accept agrifood nanotechnology were found to be the results of complex feedback structure. This study suggests several consumer policy and programmatic levels in the system toward enhancing consumer acceptance of agrifood nanotechnology products where warranted.