A “soft” electrochemical method has been developed to deprotonate propylammonium-functionalised mesoporous silica particles and to exploit the resulting amine-functionalised material in carbon paste electrodes in the “open-circuit accumulation–voltammetric detection” sequence, using Cu(II) as the target analyte. The method is based on shifting the ammonium-amine acid–base equilibrium to the right via the electrochemical reduction of protons arising from the dissociation of ammonium moieties in aqueous medium. This approach is less destructive than the “classical” chemical deprotonation involving the use of hydroxide ions, resulting in much higher sensitivity with respect to Cu(II) preconcentration and detection. Possible generalisation of the electrochemically induced improvement of the binding properties of silica-based organic–inorganic hybrids was then illustrated through the use of carbon paste electrodes modified with carnosine-functionalised silica applied to Cu(II) detection with enhanced sensitivity and selectivity.