Abstract Solid oxide fuel cell research and development has faced challenges with slow startup, slow shutdown and a limited number of thermal cycles, which hinders the technology in areas like micro-combined heat and power. A novel micro combined heat and power system, based on a boiler/hot water heater with integrated micro-tubular flame assisted fuel cells (mT-FFCs), is proposed which requires rapid startup, shutdown and thousands of thermal cycles. A 9 cell mT-FFC stack is developed and operated in a two-stage combustor. Rapid startup and shutdown of the fuel cells is demonstrated. The first-stage combustor is ignited, turned off and re-ignited for a total of 3000 on/off, thermal cycles. A maximum heating rate of 966 °C.min −1 and a maximum cooling rate of 353 °C.min −1 is achieved while thermal cycling. Despite the presence of CO in the exhaust, the anode remains porous and crack free after ∼150 h of thermal cycling testing. The mT-FFC stack continues to generate significant power, even after completing the cycling test, and a low voltage degradation rate is reported.