Summary Root microbiota composition shifts during the development of most annual plants. Although some perennial plants can live for centuries, the host–microbiome partnerships and interaction mechanisms underlying their longevity remain unclear. To address this gap, we investigated age‐related changes in the root metabolites, transcriptomes, and microbiome compositions of 1‐ to 35‐yr‐old Populus tomentosa trees. Ten co‐response clusters were obtained according to their accumulation patterns, and members of each cluster displayed a uniform and clear pattern of abundance. Multi‐omics network analysis demonstrated that the increased abundance of Actinobacteria with tree age was strongly associated with the flavonoid biosynthesis. Using genetic approaches, we demonstrate that the flavonoid biosynthesis regulator gene Transparent Testa 8 is associated with the recruitment of flavonoid‐associated Actinobacteria. Further inoculation experiments of Actinobacteria isolates indicated that their colonization could significantly improve the host's phenotype. Site‐directed mutagenesis revealed that the hyBl gene cluster, involved in biosynthesis of an aminocyclitol hygromycin B analog in Streptomyces isolate bj1, is associated with disease suppression. We hypothesize that interactions between perennial plants and soil microorganisms lead to gradual enrichment of a subset of microorganisms that may harbor a wealth of currently unknown functional traits.