The most comprehensive and inclusive estimates for the economic burden of foodborne illness yield values as high as $97.4 billion USD annually. However, broad incidence and cost estimates have limited use if they cannot be attributed to specific foods, for the purposes of food safety control. In this study, we estimated the economic burden of foodborne illnesses resulting from flour and flour-based food products in the United States from the years 2001 to 2021. The outbreak, illness burden, and health economic data are combined to generate these estimates. Our model combined outbreak data with published Centers for Disease Control and Prevention multipliers to estimate the annual number of illnesses associated with flour-borne pathogens. We then integrated illness severity data with an updated economic model that accounts for costs related to medical care, productivity loss, loss of life, along with the quality of life loss that entails pain and suffering. In total, 752 cases and 223 hospitalizations from flour-related illnesses were reported from 2001 to 2021, with an average of 37.6 cases of reported cases annually. However, the actual number of cases, accounting for underreporting and underdiagnosis, can be as high as 19,440 annually. Pathogens involved in these outbreaks are Salmonella, E. coli O157:H7, and E. coli O121. Our estimates suggest average annual economic losses, including healthy years of life lost, of $108 and $258 million using two alternative models.