Systems and methods are provided for operating molten carbonate fuel cells to allow for periodic regeneration of the fuel cells while performing elevated CO2 capture. In some aspects, periodic regeneration can be achieved by shifting the location within the fuel cells where the highest density of alternative ion transport is occurring. Such a shift can result in a new location having a highest density of alternative ion transport, while the previous location can primarily transport carbonate ions. Additionally or alternately, periodic regeneration can be performed by modifying the input flows to the fuel cell and/or relaxing the operating conditions of the fuel cell to reduce or minimize the amount of alternative ion transport.