This study modeled the kinetic data of swine wastewater characteristics in microbial fuel cells (MFCs), including conductivity, chemical oxygen demand (COD), volatile fatty acids (VFAs), total ammoniacal nitrogen (TAN), nitrite, nitrate, and phosphate concentrations. The removals of VFA and TAN were efficient, indicated by the short half-life times of 4.99 and 7.84 d, respectively. Among the removed TAN, 13.6% was recovered from the evaporated air outside of MFC cathode, indicating its potential use for ammonium recovery from animal wastewater. The mechanism for phosphate removal was principally the salt precipitation from cathode, and the removal needed improvement as it was far from completion even after 42 d operation. MFC with an external resistor of 2.2 kΩ and fed with swine wastewater generated relatively small power (28.2 μW), energy efficiency (0.37%) and Coulombic efficiency (1.5%). The main reason for the impaired performance was the inhibitory effects caused by TAN on Pt activity and VFA on anodic biofilm activity. Dilution of swine wastewater dramatically improved the power generation as the inhibitory effect was reduced. Zeolite and granular activated carbon were effective in the selective adsorption of ammonia or organic matter in swine wastewater, and so substantially improved the power generation, energy efficiency, and Coulombic efficiency. A smaller external resistor in the circuit was also observed to promote the organic matter degradation and shorten the required reaction time in the batch mode.