Soil microbes are influenced by their environment, and soil pH is well known as a driver of community structure, including within the plant root zone. However, the effect of pH induced changes on root-associated microbial communities for plant growth, resource allocation, and disease resistance is not well understood, especially for long-lived woody plants. In this study, we examined whether soil microbial communities altered by soil pH could affect tree growth, resource allocation, and resistance to a soil-borne pathogen. In a controlled greenhouse setting, we treated Fagus grandifolia saplings with small amounts of forest soil that had been manipulated to alter soil pH and microbial communities. In addition, 1-yr after inoculation with forest soil, half of the trees were also inoculated with the root rot pathogen Phytophthora cinnamomi to induce physiological stress . Tree growth showed no response to treatment with forest microbes; however, P. cinnamomi altered resource allocation, leading to increased ratios of aboveground to belowground biomass for trees treated with forest microbes. Interestingly, trees grown in pasteurized soil had a tendency toward the opposite pattern of reduced ratios of aboveground to belowground biomass. Soil treatment and pathogen inoculation interacted to alter water transport tissues; stems grown with microbes from acidic forest soil had higher vessel density when challenged with P. cinnamomi , while trees grown with microbes from neutral forest soil had higher vessel density in the absence of the pathogen. Our study suggests that the composition of root-associated microbes can affect resource allocation under stressful conditions for long-lived woody plants.