During recent decades, forest ecosystems have been exposed to high levels of atmospheric pollution, and it has been argued that this affects the composition and activity of decomposer communities and, subsequently, ecosystem functioning. To investigate the effects of atmospheric pollution on protozoa and microflora, a new experimental design was used. Undisturbed soil columns, originating from six coniferous forests across Europe and representing different stages of soil acidification, were transferred to two Scots pine forests (Fontainebleau and Wekerom) with different levels of N and S deposition (NH4 +-N=4.90 and 42.50 kg ha–1 year–1; SO4 –S=10.90 and 30.40 kg ha–1 year–1, respectively). The number of protozoa, microbial biomass C and microbial activity were estimated in the organic layer (Of) of the transferred soils at the two host sites after 21 months of incubation. The experiment aimed at answering two questions: (1) Do changes in environmental conditions, studied by transferring soils from one site to another, affect protozoa and microbial communities and, if so, (2) how important are changes in both N and S deposition in explaining the effects of soil transfer on protozoa and microbial communities? The interaction between protozoa and microbial communities was addressed with regard to these changes in environmental conditions. No effect of enhanced N or S deposition on protozoan numbers and microbial biomass C, basal respiration and caloric quotient was revealed. Reciprocal transfer of various soil columns resulted in lower abundance and activity of protozoa and microbes. This reduction could not be explained by differences in N and S deposition, but by differences in microclimate and adaptation. In some cases, protozoa correlated with pH, C/N ratio, P and S content and leached mineral N.