Wheat-based foods has emerged as another potential vehicle for foodborne illness in humans. The recent occurrence of recalls involving wheat-based foods requires a full understanding of how these pathogens thrive in these food products and developing potential intervention strategies to address pathogen contamination. This manuscript is the second of a two-part review covering the status of the food safety of wheat-based products. In this manuscript, available information on the survival of enteric foodborne pathogens, food safety issues, and potential pathogen reduction steps on wheat-based foods were reviewed. Shiga toxin-producing E. coli and Salmonella are capable of surviving in wheat flours and grains for extended periods (≤ 2 years). Based on the food safety issues linked to wheat flour, the main enteric pathogens of concern are STEC (O157, O121, O26, and O103) and Salmonella. Diverse interventions such as tempering treatments, thermal treatments, and non-thermal technologies all effectively reduced the pathogenic loads of wheat grains and wheat flours (2 to 6 log CFU/g reduction). Addressing pathogen contamination of wheat-based foods is a major concern for the milling industry. Future studies could be focused on improving pathogen reduction performance and validating their effects against diverse product and process conditions.