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The initial microbial load of the grain is a safety concern for wheat-based products. The objective of this study were to (i) determine the impact of adding a combination of organic acid and NaCl to tempering water on the microbial load of soft wheat prior to milling, and (ii) to evaluate the impact on the microbial quality and functional properties of the resulting flour. Wheat was tempered to 15% moisture under controlled (18h, 22-24°C, 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, coliform, and <i>Enterobacteriaceae</i> (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 3.1 and 4.5 log CFU/g, respectively. After milling on a Quadrumat Jr, milled fractions were collected and sieved to separate the bran and germ from flour. Flour was evaluated by the same microbial analysis described for wheat. Additionally, flour functionality was evaluated by Rapid Visco Analyzer and Solvent Retention Capacity (SRC). The microbial load of the flour obtained from wheat tempered with lactic acid (5%)-NaCl was significantly lower (p<0.05) than the control flour and no significant differences in pasting properties among resulting flours were observed (p>0.05). In addition, there were no significant differences (p>0.05) in the SRC values among flours for the sodium carbonate solvent, which indicates that starch granules were not damaged by the tempering solutions. Addition of organic acids and NaCl in tempering water provides milled products with improved microbiological quality, without affecting functionality.