Direct and indirect effects of habitat modification and changes in biotic interactions should be taken into consideration to understand the ecological consequences of forest anthropogenic disturbance on forest ecosystems. Few empirical studies assess indirect effects and consider multiple trophic levels, but recent statistical and theoretical advances provide new paths to do so. Here, we investigate direct and indirect effects of anthropogenic disturbances on multi-trophic soil communities in a boreal forest. We assessed the short term (2 years) abiotic and biotic responses to two anthropogenic disturbance intensities: conventional harvesting and harvesting followed by organic matter removal. We quantified the changes on eight groups of species, including vegetation and soil fauna, and their potential effects on leaf litter decomposition. We used a trait-based approach and structural equation modeling to quantify direct and indirect effects of disturbance intensity on environmental conditions, functional responses of the above and below ground biotic communities and leaf litter decomposition. Forest disturbance intensity was found to have a bottom-up effect on species community composition, from lower trophic levels (for example, detritivorous springtails) up to soil fauna top predators (for example, running spiders). Our results suggested some impacts of disturbance on leaf litter decomposition through changes in faunal communities. Our study shows that a multi-trophic assessment of disturbance impacts provides an integrative understanding of ecosystem responses to environmental change.