Effects of metal contamination on soil biota activity were investigated at 43 sites in 5 different habitats (defined by substratum and vegetation type) in a post-mining area. Sites were characterised in terms of soil pH and texture, nutrient status, total and exchangeable metal concentrations, as well as plant species richness and cover, abundances of enchytraeids, nematodes and tardigrades, and microbial respiration and biomass. The concentrations of total trace metals were highest in soils developed on mining waste (metal-rich dolomite), but these habitats were more attractive than sandy sites for plants and soil biota because of their higher content of organic matter, clay and nutrients. Soil mesofauna and microbes were strongly dependent on natural habitat properties. Pollution (exchangeable Zn and Cd) negatively affected only enchytraeid density; due to a positive relationship between enchytraeids and microbes it indirectly reduced microbial activity. ► Bioavailable zinc and cadmium reduce enchytraeid density. ► Enchytraeids positively influence microbial respiration and biomass. ► Total contents of heavy metals in soil are poor predictors of the distribution of plants and soil biota. Elevated concentrations of exchangeable Zn and Cd reduce enchytraeid density and indirectly affect microbial activity adversely.