The objectives of this study were to inactivate the enzymes α-amylase, lipase, protease, and peroxidase in flour with supercritical carbon dioxide (scCO2), and to optimize the enzymatic treatment conditions. Enzyme inactivation is important, due to the undesirability of certain flour enzymes that cause adverse reactions during storage as unpleasant rancidity of flour, and, at the same time, reduce the shelf life of flour. Therefore, crude enzymes and flour were initially exposed to scCO2 to determine the effect on specific enzyme activity under appropriate conditions. The activity of the unwanted enzymes lipase and peroxidase decreased under optimal process conditions of scCO2 exposure, lipase by 30%, and peroxidase by 12%, respectively. It was discovered that the inactivation of enzymes in wheat flour occurred, where, at the same time, this sustainable method allows the regulation of enzyme activity in the baking process. Afterwards, the effect of scCO2 on the physicochemical properties of flour, morphological changes on starch granules, and content of total lipids was studied. In scCO2-treated white wheat flour, the fat content decreased by 46.15 ± 0.5%, the grain structure was not damaged, and the bread as the final product had a lower specific surface volume. Therefore, this could be a promising technology for flour pretreatment, potentially impacting the prolonging of its shelf-life.