Restored ecosystems typically lack the diversity of undisturbed old-growth ecosystems, but we lack a comprehensive understanding of why this might be the case. One possibility is that previous land-use can leave long-lasting changes to soil microbial communities. We have found that many species of conservation concern are highly reliant on mutualisms with soil microorganisms, including mycorrhizal fungi and rhizobia, and meeting conservation goals may require re-establishing these mutualisms in degraded soils.