Cobalt (Co) recycling from the spent LIBs not only favors the ecological protection also meets the supply chain of Co in the international market. In this research, a three-dimensional microbial-fuel-cell (3D-MFC) two-chamber system with granular activated carbon (GAC) microelectrodes was constructed to remove and recover Co from the stripping cobalt sulfate solution. The 3D bio-electrochemical (BE) system exhibited the largest voltage output and power production at 12th day during the acclimation, achieving the maximum power densities (W/m(3)) of 6.24, 10.29, 14.52, 12.59, and 8.78, respectively. The GAC prepared at 500 degrees C achieved highest removal and recovery efficiencies of Co in the 3D-MFC system. The maximum removal efficiency of 98.47%, the recovery efficiency of 96.35%, the power density of 11.34 W/m(3), and the columbic efficiency of 28.74% were obtained in the orthogonal experiments. The influence of the operating time on the removal and recovery of Co was more obvious than the electro-output of the system. The addition of ammonium carbonate to the 3D-MFC systems clearly increased the precipitation of Co. The stacking of GAC particles in MFC had strengthened the adsorption of Co ions by intensifying the acidic-alkaline pathways during the 3D BE process. The removal and recovery of Co ions from the stripping solution in the 3D-MFC experiments were mainly achieved by the electromigration, electrostatic adsorption of GAC, and chemical precipitations of cobalt hydroxide and cobalt carbonate. A continuous process was suggested for the 3D-MFC application integrating to the traditional recovery procedure of Co from the spent LIBs at the pilot scale.