Land-use intensification can lead to taxonomic and/or functional homogenization of biotic communities, with potential consequences for ecosystem functioning. In boreal forests, managers are increasingly considering intensifying woody biomass removal for bioenergy, but associated functional effects on soil fauna that use microhabitats associated with this biomass remain poorly understood. Two years after harvesting, we assessed the effects of an increasing intensity gradient of biomass removal in a northeastern Ontario jack pine (Pinus banksiana) stand on the functional structure of Collembola and Oribatida communities, two abundant soil taxa. The gradient ranged from (1) uncut forest to (2) stem-only harvesting to intense biomass removal through (3) whole-tree harvesting (stem, top and branches) with (4) stump removal and (5) additional removal of organic soil strata. Morphological and life-history response traits associated with hypothesized functions were measured to determine changes in the functional structure (species trait diversity and composition) of communities in response to the gradient and related environmental changes. We found that functional structure of communities of both taxa was overall significantly modified by biomass removal through a compositional shift in species traits in comparison to uncut forest. Functional homogenization was observed for Oribatida communities with a loss of species that were surface-dwelling, larger, predominantly sexually reproducing and mostly micro-detritivorous. In contrast, Collembola communities were less affected with only the most extreme treatment showing a more homogenized community than the uncut forest. These functional changes were mainly explained by fewer suitable microhabitats, characterized for example by a more stable microclimate as well as more abundant and diverse food resources, due to the disturbance of forest floor organic cover with harvesting. To improve sustainable management of boreal forests, long-term studies will be needed to assess if partial functional homogenization of soil mesofauna by intensive practices persists through time and may influence soil ecosystem function.