Energy transition currently brings focus on fuel cell micro-combined heat and power (mCHP) systems for residential uses. The two main technologies already commercialized are the Proton Exchange Membrane Fuel Cells (PEMFCs) and Solid Oxide Fuel Cells (SOFCs). The pollutant emissions of one system of each technology have been tested with a portable probe both in laboratory and field-test configurations. In this paper, the nitrogen oxides (NOx), sulphur dioxide (SO2), and carbon monoxide (CO) emission levels are compared to other combustion technologies such as a recent Euro 6 diesel automotive vehicle, a classical gas condensing boiler, and a gas absorption heat pump. At last, a method of converting the concentration of pollutants (in ppm) measured by the sensors into pollutant intensity per unit of energy (in mg/kWh) is documented and reported. This allows for comparing the pollutant emissions levels with relevant literature, especially other studies conducted with other measuring sensors. Both tested residential fuel cell technologies fed by natural gas can be considered clean regarding SO2 and NOx emissions. The CO emissions can be considered quite low for the tested SOFC and even nil for the tested PEMFC. The biggest issue of natural gas fuel cell technologies still lies in the carbon dioxide (CO2) emissions associated with the fossil fuel they consume. The gas absorption heat pump however shows worse NOx and CO levels than the classical gas condensing boiler. At last, this study illustrates that the high level of hybridization between a fuel cell and a gas boiler may be responsible for unexpected ON/OFF cycling behaviours and therefore prevent both sub-systems from operating as optimally and reliably as they would have as standalone units.