A growing demand for renewable carbon (C) has led to intensified forest management resulting in the use of forest residues (e.g. canopy, bark or litter layer) as energy sources with potential modifications of soil properties and tree productivity. Because microbes mediate the recycling of C and nutrients sequestered in organic matter, we investigated the effects of organic matter (OM) removal on soil properties, root surfaces, microbial functions and abundance using a new observational forest network. We compared leaf litter and logging residue removal plots to reference plots in six beech forests located in the northern half of France. After three consecutive years of OM removal, C and nitrogen (N) pools were not affected, but OM exportation decreased the cation exchange capacity and available phosphorus (P) pool by respectively 12% and 30% in the topsoil (0–5 cm depth). Fine root surface area significantly increased by 21% in the subsoil (5–10 cm depth) in response to OM removal. Enzymatic activities involved in N and P mobilisation decreased from 12 to 38% with the manipulation of OM. Community-level profiling (CLPP) based on BIOLOG approach revealed that the metabolic potential of the microbial community strongly decreased in response to OM removal. Our results indicated that intensive forestry could affect microbial functions implicated in nutrients mobilisation. We demonstrated that soil organic matter (SOM) content is a predictor of microbial functions resistance to forest residue removal. We recommend that intensive forestry should be reduced or limited in beech forests characterised by low soil OM contents.