The promise of microbial biological control of soilborne fungal pathogens of crops has yet to be fully realised with only a few strains commercialised and available to growers. One bottleneck is the availability of suitable methods to screen microorganisms for disease control efficacy relevant to controlling disease in the field. A 3-phase in planta pathosystem containing field soil was developed to screen 2310 microorganisms for control of Rhizoctonia root rot on wheat. Test strains were added to seeds as a suspension at planting and plant growth assessed at two weeks. Strains increasing plant height and number of roots (185) were tested in a replicated Rhizoctonia pot bioassay with five wheat seedlings grown for four weeks and assessed for plant growth and root disease. Forty-three strains (1.9% of strains tested) performed better than our benchmark strains and were reassessed in pot bioassays at three inoculation levels. These tested strains represented a wide diversity of microbial genotypes including fungi, (Trichoderma, Aspergillus and Cylindrocarpon) and bacteria encompassing four phyla (Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes). These results show that microbes can be successfully and rapidly screened directly for disease control on plants.