Wheat (Triticum spp.) is one of the most important cereal crops grown in the U.S., with an average of 50 million acres planted on an annual basis. Wheat is milled into flour or semolina, which is used to make bread, cookies, noodles, and pasta. Because some consumers eat raw flour, it is necessary for it to be free of pathogens including Escherichia coli and Salmonella enterica. The fecal matter of cattle and poultry often contains these bacteria and can contaminate wheat. Currently, there are no requirements for controlling E. coli and S. enterica in wheat, which has resulted in outbreaks of both pathogens. Thus, future research must focus on the development of processes that control these pathogens in wheat. Possibilities include feeding livestock probiotics, pasteurization, irradiation, and non-thermal plasma processing. The further development and implementation of these processes would decrease the safety risks associated with consuming raw wheat.