The occurrence of recalls involving pathogenic Escherichia coli-contaminated wheat flours show the need for incorporating antimicrobial interventions in wheat milling. The objectives of this study were to assess the efficacy of sodium bisulfate (SBS) tempering in reducing E. coli O121 (ATCC 2219) and O26 (ATCC 2196) wheat load and to evaluate the impact of effective (≥3.0 log reductions) SBS treatments on wheat flour quality. Wheat grains were inoculated with E. coli (~6 log CFU/g) and tempered (17% moisture, 24 h) using the following SBS concentrations (%wheat basis): 0, 0.5, 0.75, 1.0, 1.25, and 1.5% SBS. Reductions in E. coli O121 and O26 wheat load at different time intervals (0.5, 2, 6, 12, 18, and 24 h) during tempering were evaluated. The addition of SBS during tempering resulted in E. coli (O121 and O26) log reductions of 2.0 (0.5% SBS) to >4.0 logs (1.5% SBS) (p ≤ 0.05). SBS tempering (1.25 and 1.5% SBS) produced acidic wheat flours (pH = 4.51–4.60) but had comparable wheat flour properties in terms of composition, dough, and bread-making properties relative to the control (0% SBS). SBS tempering reduced the E. coli O121 and O26 load of wheat after tempering with minimal effects on wheat flour quality.