CO2 capture and sequestration (CCS) from stationary flue gas sources is one of the critical technologies needed as the future energy landscape shifts to low carbon intensity energy systems. Molten carbonate fuel cells (MCFCs) have the potential to capture CO2 from flue gas at higher thermal efficiency than traditional CCS technologies while simultaneously producing electricity. Herein, we present an investigation of molten carbonate fuel cell behavior at carbon capture conditions using simulated natural gas combined cycle flue gas. Measurements at these low CO2 and high current conditions reveal a lower than expected cathodic consumption of CO2 Based on the strong dependence of this deviation on water partial pressure as well as mass balances revealing a net consumption of water at the cathode, a parallel oxygen reduction mechanism is proposed. In this mechanism, water and oxygen are consumed at the cathode to produce hydroxide ions which migrate through the electrolyte to the anode. This parallel mechanism contributes to power generation but not to CO2 capture. Mass transport limitations in the molten carbonate fuel cell cathode were identified as the primary driver for this alternative mechanism which were heavily influenced by the design of the current collector and cathode interface.