Functional properties of cowpea flour from seeds micronised at two different surface temperatures (130 and 170 °C) were studied. Micronisation (130 and 170 °C) significantly ( P ⩽ 0.05) increased the water absorption capacity and least gelation concentration of the flour. The treatment significantly ( P ⩽ 0.05) reduced the water solubility and swelling indices, gel strength and foaming capacity of the flour. The changes in cowpea flour functional properties, such as the loss of foaming capacity in flours from micronised (130 and 170 °C) seeds, were associated with significant ( P ⩽ 0.05) increase in the surface hydrophobicity and cross-linking of the cowpea protein. SDS–PAGE of the protein-rich fractions revealed changes in the protein subunit profile which included the formation of disulphide bonds and possibly Maillard cross-links. The flour from M-170 °C seeds was significantly ( P ⩽ 0.05) darker than was the flour from unmicronised and M-130 °C seeds.