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Reducing microbial contamination in wheat is desirable to ensure consumer safety. The purpose of this study was to determine the efficacy of adding organic acids and NaCl to tempering water to reduce microbial load in hard wheat prior to milling, and to determine the impact that these treatments might have on the microbial quality and functional properties of straight-grade and whole grain flours. Wheat was tempered to 15.5% moisture under controlled (24h, 73-75°F, 60% RH), aseptic conditions by adding water (control) or tempering solutions containing acid (acetic or lactic; 2.5% and 5% v/v) and NaCl (26% w/v). Wheat was analyzed before and after tempering for Total Plate Counts (TPC), yeasts, molds, and Enterobacteriaceae (Eb). The microbial load of the tempered wheat was significantly reduced by all organic acid-NaCl treatments (p<0.05). The combination of lactic acid (5%) and NaCl was the most effective against TPC and Eb (p<0.05), with an average reduction of 3.5 and 4.7 log CFU/g, respectively. After experimental milling, fractions were collected and recombined to obtain straight-grade or whole grain flours. All combinations of organic acid-NaCl were effective in reducing the microbial load of the final milled product (p<0.05). Even though some significant differences in mixing properties were observed, their impact on functionality was minimal. Only whole grain flour from wheat tempered with acids at 5% required longer times (5.3 min) for optimum dough development compared to the control (4.5 min). Straight-grade flour obtained from all treatments showed higher maximum force for mixing than the control flour. Additionally, dough mixing tolerance in both flours was not affected, regardless the acid level. Implementation of organic acids and NaCl in tempering water provides milled products with improved microbiological quality, without compromising functionality.