Biomass waste from jackfruit and durian were used to produce carbon aerogel electrodes incorporating stable scaffolding of base material and natural nitrogen doping. Higher atomic doping of nitrogen in DCA (durian carbon aerogel) compared to JCA (jackfruit carbon aerogel) indicates preservation of nitrogen-containing functional groups during the synthesis. The specific surface area and proportion of mesopores is greater for DCA than for JCA samples. Electrochemical characterizations via cyclic voltammetry, galvanotactic charge discharge and electrochemical impedance spectroscopy show high specific capacitance for both DCA (591 F g−1) and JCA (292 F g−1) at 1 A g−1 current density with two-electrode configuration with excellent cycling stability and charge.