Microbiomes can dramatically alter individual plant performance, yet how these effects influence higher order processes is not well resolved. In particular, little is known about how microbiome effects on individual plants alter plant population dynamics, a question critical to imperiled species conservation. Here, we integrate bioassays, multidecadal demographic data, and integral projection modeling to determine how the presence of the natural soil microbiome underlies plant population dynamics. Simulations indicated that the presence of soil microbiomes boosted population growth rates (λ) of the endangered Hypericum cumulicola by 13% on average, the difference between population growth versus decline in 76% of patches. The greatest benefit (47% increase in λ) occurred in low nutrient, high elevation habitats, suggesting that the soil microbiome may help expand H. cumulicola’s distribution to include these stressful habitats. Our results demonstrate that soil microbiomes can significantly affect plant population growth and persistence, and support the incorporation of soil microbiomes into conservation planning. plant population growth and persistence, and support the incorporation of soil microbiomes into conservation planning.