The effect of heat treatment (130 °C surface temperature) of pre-conditioned (20 or 53% moisture) bambara groundnut seeds using infrared, microwave energy alone and in combination on functional properties of their flours were determined. Heat treatment caused reduction in water and nitrogen solubility indices of resulting flours. There was a combination effect of moisture conditioning, heat treatment and treatment time. Heat treatment caused starch pre-gelatinisation and denatured protein in resulting flours, which significantly increased with moisture level and treatment time. Endothermic peak by DSC decreased with increased treatment time for all heat treatments in flours from 53% moisture level seeds but not in 20% moisture level seeds. Pasting temperature of bambara groundnut flours significantly increased with heat-treatment times (0,5 and 10 min), but final paste viscosities decreased. Resulting flours from the combined treatment had a more significant reduction in pasting viscosities at both moisture levels than those resulting from infrared or microwave heat treatment. The low viscosity may be explained by unavailability of starch to form a viscous paste due to surrounding protein matrix around the starch granules. Resulting flours had low viscosities, this should be considered when compositing bambara groundnut to wheat for composite bread production.