We investigated the response of soil microbial communities in tropical ecosystems to increased nutrient deposition, such as predicted by anthropogenic change scenarios. Moderate amounts of nitrogen and phosphorus and their combination were added along an altitudinal transect. We expected microorganisms and microbial grazers (testate amoebae) to significantly respond to nutrient additions with the effect increasing with increasing altitude and with duration of nutrient additions. Further, we expected nutrients to alter grazer-prey interrelationships. Indeed, nutrient additions strongly altered microbial biomass (MB) and community structure as well as the community structure of testate amoebae. The response of microorganisms varied with both altitude and duration of nutrient addition. The results indicate that microorganisms are generally limited by N, but saprotrophic fungi also by P. Also, arbuscular mycorrhizal fungi benefited from N and/or P addition. Parallel to MB, testate amoebae benefited from the addition of N but were detrimentally affected by P, with the addition of P negating the positive effect of N. Our data suggests that testate amoeba communities are predominantly structured by abiotic factors and by antagonistic interactions with other microorganisms, in particular mycorrhizal fungi, rather than by the availability of prey. Overall, the results suggest that the decomposer system of tropical montane rainforests significantly responds to even moderate changes in nutrient inputs with the potential to cause major ramifications of the whole ecosystem including litter decomposition and plant growth.