SummaryThis study was conducted to compare the effect of lipids removal using supercrital‐CO2 extraction and organic solvents (hexane and isopropanol) from hard and soft wheat flour varieties. Flours were evaluated for physicochemical properties (protein, ash, hunter colour), sodium dodecyl sulphate‐polyacrylamide gel electrophoresis, foaming properties, water and oil absorption capacity, pasting, farinographic and dynamic rheology. Protein content of flours increased after defatting and supercritical fluid extracted (SCE) wheat flours showed the highest increase. SCE flours showed higher peak viscosity than native and hexane extracted (HE) and isopropyl alcohol extracted (IPAE) flours. Functional properties improved upon defatting and the highest increase in functional properties was observed for SCE flours. Empirical and fundamental rheological measurements were affected by defatting and SCE flours showed the highest change in visco‐elasticity. SC‐CO2 was proved better alternative technique over conventional organic solvent methods to remove lipids from flours that brought desirable changes in some functional properties.