This study interrogated straightforward ball-milling (BM) of powdered activated carbon (AC) to intensify the selective separation by capacitive deionization (CDI) primarily for SO42− with potential eco-toxicity. Depending on the BM duration (20 to 60 h) of coconut-derived AC, the prevalent shift in pore size distribution or surface charge/moieties was observed for BM-20 and BM-60, respectively, whereas synchronous modifications were noted for BM-40. In single-pass experiments (1.2/0 V) with symmetric electrodes, BM-40 notably elevated the selectivity factor of SO42− by 36 % from equimolar SO42−/Cl− mixture (2 mM each). Enumerated effective pores for SO42− (0.76–1.1 nm) and shorted diffusion length of reduced grain accelerated replacement of pre-sorbed Cl− by divalent SO42− under the alleviated ion-sieving effects. Comparison with asymmetric cells with the pristine negative electrode further evinced that ameliorated co-ion repulsion from the oxidized (with augmented potential of zero charge) negative electrode could secure driving potential on the positive electrode to strengthen the energetic-affinity-based ion swapping. In addition, quasi-absolute selectivity for NO3− sorption (with a partial inversion behavior for Cl−) was observed in the asymmetric cell receiving equimolar SO42−/Cl−/NO3− composite. Consequently, the BM effectively regulated not only the perm-selectivity, but also the surface charge and/or specific interaction.​