Molten carbonate fuel cells (MCFCs) are operated to provide enhanced CO2 utilization. This can increase the effective amount of carbonate ion transport that is achieved. The enhanced CO2 utilization is enabled in part by operating an MCFC under conditions that cause transport of alternative ions across the electrolyte. The amount of alternative ion transport that occurs during enhanced CO2 utilization can be mitigated by using a more acidic electrolyte.