This study explores an innovative electrochemical strategy for the removal of the highly stable and toxic EDTA-Ni complex found in electroplating wastewater. Utilizing a cobalt-based single-atom catalyst (Co-NC) in an electro-enhanced system, we achieved significant activation of peroxydisulfate (PDS) for effective degradation of EDTA-Ni. Under optimal conditions of 40 mA current density and a pH range of 3–7, more than 97% of EDTA-Ni (1 mM) was successfully degraded within 90 min. Through detailed electrochemical experiments, we identified that atomic hydrogen (H*) played a crucial role in the indirect activation of PDS, facilitating the formation of reactive sulfate radicals (·SO4-). Computational analysis using density functional theory (DFT) confirmed that the H*-mediated reduction pathway had a notably low energy barrier (ΔGbs = 0.51 eV), making it the dominant activation mechanism. Gas chromatography-mass spectrometry (GC–MS) further revealed the primary degradation intermediates, providing insights into the breakdown process of EDTA-Ni. This research underscores the potential of Co-NC catalyst as a highly effective catalyst for treating persistent heavy metal complexes in advanced oxidation systems.