In windthrow-affected areas, the research of biota is of high relevance taking into account the lack of knowledge about the dynamics of their flora, soil properties, and tree stand regeneration. An important task is to study the mechanisms of the natural dynamics of plant communities after major disturbances in large boreal forests. This paper was aimed to investigate the effects of a total windthrow event on the dynamics of biodiversity in pristine mid-boreal spruce (Picea abies) forests. The study was carried out in the Vodlozersky National Park (Northwest Russia: Arkhangelsk Region and Republic of Karelia), situated in the northern and middle taiga subzones. A series of permanent sample plots was established in an area affected by massive windthrow in 2000. The windthrow consequences of the forest communities have been studied, starting from the year of the event (2000) at 2–5-year intervals. A soil survey has been conducted in 2016. Windthrown trees, situated in the sample plots, were counted by species and diameter classes. Natural regeneration was estimated in subplots with a division to height cohorts and vitality status. Geobotanical relevé sampling of the ground vegetation has been conducted in 1 × 1-m permanent plots. Aphyllophoroid fungi (Basidiomycota) were counted by fruit bodies. Main soil pits and partial pits were dug. The morphological description of soils was produced in both undisturbed and disturbed sites in the study area. Obtained data, covering 20 years of surveys of various components of the forest plant communities (tree stand, advance regeneration, ground vegetation, wood-destroying fungi, soils), were analysed. We found that 16–20 years after the windthrow event the species and age structure of the tree stand has been considerably changed due to the forest stand rejuvenation. Post-windthrow regeneration of coniferous species in the true-moss group of forests has been successfully going on. By the end of the second decade after the windthrow event, cowberry spruce forests contained 4300 individuals/0.01 km2 of viable spruce regeneration, including 1500 individuals/0.01 km2 belonging to the large size category of spruce trees. In the bilberry-Sphagnum-type forest, spruce regeneration amounted to 8700 individuals/0.01 km2, including 2200 individuals/0.01 km2 belonging to the large size category of spruce trees. This amount is sufficient to ensure the development of spruce-dominated communities in the future. Since the forest ecosystems were recovering after the windthrow, the biodiversity of changed, that was reflected in an increase in the species composition of the ground vegetation and fungal communities. Over the study period (2001–2021), surveys of the sample plots demonstrated 83 aphyllophoroid fungi species, including five species included in the Red Data Book of the Republic of Karelia, as well as 22 taxa, considered old-growth forest indicator- and specialist species. The number of wood-destroying fungi species was the highest in the period from the 12th to the 19th post-windthrow years. The changes in soil properties on windthrow-affected sites were more explicit in the upper horizons: soil acidity decreased; both potassium and carbon content increased; nitrogen distribution across horizons became more even. An increase in the carbon-nitrogen ratio was detected in the Е and BF horizons. The obtained data can be used for predicting the regeneration of pristine mid-boreal spruce forests affected by catastrophic disturbances.