Protists, in particular bacterivores, are essential players in the rhizosphere; thus, how their interactions with bacteria and fungi affect plant productivity and soil nutrient cycles warrants more attention. Using next-generation sequencing of the 18 S rRNA gene, we investigated the distribution of two major protistan phyla, Cercozoa and Endomyxa, across four seasons, and four soil compartments – rhizosphere, root, soil and litter. The sampling was replicated in two forests in Norway and the Czech Republic, in order to test our results across biogeographic scales. Compartment had a major influence in shaping protistan communities, over and above spatial distance and seasonal variation. Protistan diversity was highest in the bulk soil while lowest in the roots, suggesting that the plants select for restricted assemblages of protists. Accordingly, only the root compartment harboured a subset of the bulk soil protistan diversity. In addition, protistan communities showed markedly different distributions according to their feeding modes, with opposite patterns for bacterivores versus omnivores and eukaryvores. The small bacterivorous flagellates (mostly Glissomonadida) were more abundant in roots, while the larger amoeboid eukaryvores (e.g. some of the Cryomonadida and vampyrellids) dominated in soil and in the rhizosphere, and the omnivores (e.g. Euglyphida and part of the Cercomonadida), also large and mostly amoeboid, were more abundant in litter. The current view of the soil microbiome is mostly focused on bacteria and fungi: this detailed study on the community distribution of protists according to their feeding modes reveals the essential role they play in each of the soil compartments, an essential precondition for a detailed understanding of the soil food web and nutrient cycling in forest.