The effects of tempering with phosphoric acid (PA) and potassium carbonate (PC) solutions on the microbial load and the quality of wheat flour and fresh noodles (FNs) were studied. With the increase of PA/PC concentration, total plate count (TPC) and mold and yeast count (MYC) of tempered wheat kernels and flour streams decreased significantly (p < 0.05), and 3B and 3M flour streams had the greatest microbial reduction. PA/PC tempering had little effect on grinding characteristics of wheat kernels. Specifically, the whiteness of the obtained straight-grade flour increased and polyphenol oxidase (PPO) activity decreased significantly (p < 0.05) and the pH and acidity changed slightly. RVA and Mixolab showed that the pasting viscosity decreased slightly after PA tempering, and the protein strength increased slightly after PC tempering. The initial microbial quantity and browning rate of FNs made from flour obtained from wheat tempered with PA/PC solutions decreased significantly (p < 0.05) and the texture characteristics of FNs were significantly enhanced (p < 0.05). The results showed that tempering with PA/PC solutions could effectively reduce the microbial content of flour streams without detrimental effects on the quality of flour and FNs.