Bacillus species such as Bacillus subtilis and Bacillus amyloliquefaciens are widely used to produce fermented foods from soybeans and locust beans in Asian and West African countries, respectively. Genomic information for B. subtilis strains isolated from Asian Bacillus-fermented foods (BFFs) has been gathered, and the chemical components of fermented products were defined with metabolomic approaches, facilitating the development of new starter strains and the evaluation of health claims. On the other hand, although advanced studies have been performed for some commercially produced BFFs, home-manufactured products still remain to be characterized in rural areas. In West Africa, the microbial flora of BFFs was examined in detail, leading to the isolation of candidates of the starter that produced bacteriocin against Bacillus cereus contaminating the products. These studies may provide a choice of Bacillus strains in food application and increase opportunities for further usage of Bacillus in foods.