To quantify the capacity fade mechanism in lithium ion batteries composed of a spinel-based cathode and an artificial graphite, a comprehensive mathematical model describing the cycling performance of LiMn2O4/graphite lithium ion cell is developed in this work. The developed model is incorporated into the Newman’s Porous Composite Electrode framework (PCE) and implemented in the battery module of COMSOL Multiphysics. The proposed model is used to investigate the effects of variations in the ambient temperature and of voltage range of cycling on the capacity fade. The effect of changes in the volume fraction of cathode active material, resistance in the cell and state of charge are also studied.