There has been much more damage to forests in the Slovak Republic in the second half of the 20th century than to other European countries. Forested mountain massifs have become a filter of industrial and transportation emissions from abroad, as well as from domestic origins. There are not only acidic deposits of sulphur and heavy metals present in forest soils, but other additional environmental problems, such as climate change, storms, fires, floods, droughts, are worsening the situation. Therefore, forest terrestrial ecosystems are becoming more vulnerable due to changes in natural and environmental conditions. In the High Tatra Mountains in Slovakia, which are protected as a national park, four internationally monitored localities were established after the windthrow disaster in 2004 and fire in 2005: REF, with intact forest; EXT, with extracted wood mass; NEX, with non-extracted wood mass; and FIR, the burnt locality. Soils from these localities were microbiologically analysed with special attention to fungi. Bacterial microbiota detected by high-throughput sequencing showed the prevalence of the genera Acidothermus, Mycobacterium, and Nocardia, and a very low presence of the genera Acidibacter, Burkholderia-Paraburkholderia, Optitus and the uncultured genus Desulfurellaceae H16 in the soil sample from the burnt locality when compared with the unburned sites. Additionally, soil mycocoenoses showed a low similarity between the locality with an intact forest ecosystem and the localities with extracted (REF–EXT) and non-extracted (REF–NEX) wood mass. There was no similarity with the burnt locality (FIR), where heat-resistant fungi dominated. It was shown that the windthrow disaster and subsequent extraction or non-extraction of wood mass did not affect the soil microbial communities or their development. On the other hand, the influence of fire was significant.