Agriculture and horticulture worldwide faces a dilemma: fungal pathogens cause severe economic and yield losses, yet fungal pathogens are rapidly evolving mechanisms of resistance to chemical fungicides used to control them. Microbiological control agents, which are a living inoculum with antifungal properties, is a prospective method to complement and compensate for fungicides as their effectiveness diminishes over time. Although many biocontrol agents show promise in vitro, their ability to control pathogens often falls over in planta. The purpose of this study was to understand the behaviour of a promising biocontrol agent in situ, using modern metatranscriptomic tools. We hypothesised that with sufficient inoculum, a biocontrol agent should be able to remain within the rhizosphere, and that the powerful antimicrobial secondary metabolites it produces should have a measurable effect on the microbial consortium around it. By coating wheat seeds with spores of the Streptomyces sp. MH243, we were able to observe the proliferation and metabolism of MH243 in the rhizosphere, biosynthesis of secondary metabolites, and its effects on the microbial diversity around it, including flow-on effects such as fungal pathogen activity.