The aim of this work, focused on natural gas fired distributed power systems, is the experimental analysis of the start-up and shutdown for high temperature fuel cell hybrid systems. These critical phases have been emulated using the micro gas turbine test rig developed by TPG at the University of Genoa, Italy. The rig is based on the coupling of a modified commercial 100 kWe recuperated gas turbine with a modular volume designed to emulate fuel cell stacks of different dimensions. It is essential to test the dynamic interaction between the machine and the fuel cell, and to develop different operative procedures and control systems without any risk to the expensive stack. This paper shows the preliminary experimental results obtained with the machine connected to the volume. The attention is mainly focused on avoiding surge and excessive stress on the machine components during the tests. Finally, after the presentation of the valve control system, this paper reports the emulation of the hybrid system start-up and shutdown phases. They have been performed to produce a gradual heating up and cooling down of the fuel cell volume, using the cold bypass line, three high temperature valves, and the machine load control system. This approach is necessary to avoid high thermal stress on the cell material, extremely dangerous for the plant life.