Auxiliary power units (APUs) running on carbon-containing fuels provide solutions for high-efficient power supply and emission reduction. In order to ensure safe operation, unwanted degradation caused by carbon depositions should be avoided or controlled. Early detection allows trigerring of counteractions and avoids rapid deterioration of the cell performance as well as mechanical degradation of the cell microstructure and it is presented here. This study also shows that carbon does not only block the active catalyst sites and porous gas channels thus deteriorating the cell performance, but massive carbon depositions lead to destruction of the lattice YSZ-structure. In order to prolong the lifetime of the investigated cells, carbon-dioxide is tested as a possible agent for gasification of deposited carbon. Supplying with CO2 gasifies carbon to carbon-monoxide, but experimental investigations show further degradation of the cell performance and a reduced methane conversion rate. A method, which represents a combination of CO2 fed to the anode and an overvoltage applied to the cell, enabled complete performance regeneration in a cell-protecting manner. (C) The Author(s) 2016. Published by ECS. All rights reserved.