Functional properties of flours from pre-soaked and micronised (130 °C) whole and dehulled bambara seeds (5, 10 and 15 min) were determined. An increase in micronisation time significantly reduced the pasting viscosity of the flours. Significant reductions in the differential scanning calorimetry endothermic peak enthalpies and loss of birefringence in the starch were found, indicating starch pre-gelatinisation when micronised. The low viscous paste of resultant flours seems to be related to protein denaturation as shown by decrease in nitrogen solubility index. Starch was embedded in a protein matrix as shown by confocal laser scanning microscopy. This denatured protein matrixes could be in part preventing starch hydration and dispersion during pasting and thus reduced viscosity. Dehulling reduced the pasting viscosity suggesting higher effect of micronisation for dehulled than whole samples. Resulting flours can be useful ingredients in protein energy-dense foods due to low viscosity.