While established in Asia, rice koji and miso are fermented foods that are becoming more popular in western countries. They have been shown to contain a variety of microorganisms, consisting of bacteria, yeasts, and fungal species. Many contemporary miso varieties are not pasteurized as consumers are looking for more natural products, and/or have the desire to consume fermented foods containing live microorganisms. While correctly prepared fermented foods are rarely associated with food safety outbreaks, incidences have been recorded. On these occasions, pathogenic, or spoilage microorganisms were introduced into the products from external sources such as the raw material or the processing environment. Consequently, hygiene and fermentation conditions need to be carefully monitored to ensure food safety. Furthermore, many of the production steps during koji and miso manufacture do not fit into contemporary food safety guidelines for foods. Although pH is a required food safety hurdle for fermented foods, this does not apply to nonacidic foods such as koji or miso. This review focuses on control of microbial pathogens and discusses the processes of miso fermentation, and how fermentation of rice koji and miso fits with current food safety hurdles in western countries.