There are a number of ways to clear the aftermath of a windthrow disturbance of forest stands, the most common practice being to remove all broken trees and broken-off crowns lying on the ground. This practice leads to complete exposure of the soil, which deprives soil invertebrates (including Collembola) of the protection of trees that affords them a chance of surviving. Accordingly, following a windthrow disturbance of pine stands in 2017, a three-year study of collembolan assemblages was undertaken in stands spared from salvage logging. We aimed to test the effect of three different levels of disturbance (severely, moderately and least disturbed stands with a canopy cover of 0–20%, 20–60% and 60–90%, respectively) on the survival of Collembola assemblages and to determine its association with changes in the soil environment and in the LAI index. Additionally, in the severely and moderately disturbed stands, Collembola were sampled between crowns of fallen trees and under the crowns. There were no significant differences in density, species richness and proportions of individuals of belowground “soil” and aboveground “epedaphic” species between the Collembolan assemblages that were associated with the degree of windthrow disturbance and time since disturbance. The study confirmed the presence of a significantly higher number of species and proportion of “epedaphic” species, and a lower proportion of “soil” species in the assemblages sampled under fallen tree crowns than between crowns. Analysis of principal response curves (PRC) yielded unexpected results as it indicated that these differences were significant only in the first year post-disturbance, thus suggesting a very short-lasting protective effect of tree crowns on Collembola, RDA analysis with preselected factors from environmental variables of interest (LAI of standing and fallen tree crowns, soil respiration, soil temperature and humidity, soil pH and soil nitrogen and carbon content) indicated the LAI index as significant for the Collembolan assemblages in the first yearpost-disturbance, soil moisture in the second year, and soil temperature in the third year. This sequence of significant indices over a three year period is compatible with the fallen crowns becoming more and more thinned as a result of needles falling off (from shade to full exposure to sunlight). We nevertheless postulate that at least some trees or their crowns lying on the ground should be left in place during clearance of windthrow-affected tree stands to facilitate restoration of the soil biota.