In this study, the pyridine and quinoline could be cometabolically degraded by phenol-cultivated Comamonas sp. strain JB(strain JB). The integration of magnetically immobilized cells of JB and an E-Fenton process into one entity has been designed to prepare a novel integration system to improve the treatment efficiency of phenol, pyridine, and quinoline in coking wastewater. The optimal pH for the integration system was 3.5. Degradation rates of phenol, pyridine, quinoline, and COD by the integration system were significantly exceeded the sum degradation rates of the single E-Fenton process and magnetically immobilized cells at the optimal voltage of 1 V. During the 6 cycles, the integration system still showed higher degradation rates than that by the single magnetically immobilized cells for all the compounds. These findings demonstrated that a synergistic effect existed between the biological treatment and the E-Fenton process, and the applied voltage in the integration system played the key roles in the synergistic effect, which not only electrogenerated HO but also improved the activity of phenol hydroxylase and strain JB concentration.