The aim of this work was to carry out long-term monitoring on the concentration and identification of phytopathogens in wood chip storage areas in urban-type heating plants. Three municipal heating plants in the central part of Slovakia were selected. The plants store biomass in large-capacity piles with a volume of 4 to 5000 m3. Samples were obtained every year in the 2017–2022 period from the surface of the piles and from a depth of 0.5 m. Their moisture content was determined in the laboratory and the microbial analysis was performed by an accredited laboratory. The average number of colonies of phytopathogens did not differ significantly in individual years. The highest number of colony-forming units per gram was achieved by the species of the genera Penicillium and Aspergillus. In terms of occurrence in individual years and the frequency of occurrence in individual samples, the most frequently recorded species were Mycelia Sterilia, Aspergillus brasiliensis, Aspergillus unguis, and Yeasts. Based on the results achieved, in the future it will be necessary to establish legislative frameworks for these risks and, at least at the national level, work procedures for individual work activities, so that the health and life of the workers of the plants, as well as residents in the vicinity of this type of plant, are not endangered.