By feeding on bacterial biomass protozoa play an acknowledged role in the liberation of nutrients in the plant rhizosphere. In addition there are suggestions that plants have mechanisms working through changes in root architecture and initiation of active release from soil organic matter, which are used to improve uptake and recirculation of nutrients in the ecosystem. All processes are carried out on a local scale in soil with roots, bacteria and protozoa interacting. The many actors and the small scale of interactions make experimentation difficult. We discuss mistakes, pit falls and misinterpretations and provide suggestions for improvement. Recent methodological progress has opened new exciting avenues for protozoan research. New techniques have already helped to reveal protozoan regulation of cooperation as well as conflict in bacterial communities. These mechanisms in turn affect bacterial functioning and target molecular control points in rhizosphere food webs in relation to plants. Integrating nutritional and regulatory aspects into new concepts of protozoan functioning in soil is a challenging frontier in protozoology.