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The soil-borne pathogen Phytophthora cinnamomi causes a deadly plant disease. Phosphite is widely used as an effective treatment to protect plants from Phytophthora cinnamomi. Phosphite as a common fungicide might influence the composition of soil fungal communities. However, whether the belowground mechanisms of phosphite-mediated protections are direct or indirectly mediated through soil biota are unknown. Therefore, exploring belowground mechanisms could contribute to the evaluation of the sustainability of phosphite use and tests hypotheses about direct versus indirect mechanisms in pathogen response. Our greenhouse pot experiment on Rhododendron species had either an after-pathogen or a before-pathogen use of phosphite to compare and evaluate plant and soil fungal responses to phosphite and the presence of an oomycete pathogen phytophthora cinnamomi. The factorial experiment also included with and without pathogen and soil biota treatments, for a test of interactive effects. High throughput sequencing analyzed the soil fungal communities, and we measured the diversity, evenness and richness of soil fungi. Phosphite effectively increased survival of Rhododendron species. It altered the composition of soil fungal communities, and the timing of using phosphite determined the way in which the fungal communities changed. Trichoderma taxa also responded to soil phosphite and Phytophthora cinnamomi. The benefits of antagonistic fungi such as Trichoderma are context-dependent, suggesting protection against pathogens depends on the timing of phosphite application. This study provides the first evidence that phosphite-mediated pathogen protection includes both direct benefits to plants and indirect effects mediated through the soil microbial community.