Waterlogged archaeological wood (WAW), approximately 4500 years old, from the prehistoric pile-dwelling settlement at Ljubljansko barje, Slovenia, was examined by scanning electron microscopy (SEM). We propose a simplified protocol for sample preparation and the SEM technique for the study of highly degraded WAW of Quercus, Faxinus, Acer, Salix and Populus, representing taxa with different wood properties. We present the advantages of the proposed technique for wood identification, the observation of various anatomical features and for the study of cell wall degradation. SEM, equipped with energy-dispersive X-ray spectroscopy (EDX), allowed us to detect significant amounts of Fe, S and Ca with different appearances, amounts and distributions in the wood of the studied taxa. In the case of Populus, an increased amount of Si was also detected. The applied SEM protocol allowed characterisation of the anatomy of the highly degraded WAW while reducing the time required for sample preparation and examination under the microscope, as well as extending the lifetime of the SEM components (e.g., tungsten filament), compared to the situation when we analyse wood samples with a greater volume.