The effect of surface oxygen on the physical and electrochemical properties of high surface area Mo, V and W carbides and nitrides has been investigated. These materials hold promise for use in supercapacitors and other electrochemical conversion devices. The carbides and nitrides were synthesized using a temperature programmed reaction method and passivated to avoid bulk oxidation on exposure to air. The passivated materials were activated in 0.3 mol dm−3 NaOH solution to remove the oxygen-rich passivation layer. This activation resulted in significant changes in the electrochemical stabilities and capacitances. The surface areas for the Mo and W-based materials were higher after activation, with the effect ranging from an 11% increase for Mo2N to a 208% increase for W2C. An increase in pore volume and mesopore density was also observed for most of the materials. Interestingly, the VC and W2C, which were electrochemically unstable in acidic electrolyte in their passivated form, were stable after activation. The capacitances of all of the materials were increased after activation with the effect ranging from 48% for Mo2N to a 79% increase for (α + β)-Mo2C. This activation process could be used to improve the performance of carbide and nitride-based supercapacitor electrode materials.