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How specific interactions between plant and pathogenic, commensal, or mutualistic microorganisms are mediated and how bacteria are selected by a plant are important questions to address. Here, an <i>Arabidopsis thaliana</i> mutant called <i>chs5</i> partially deficient in the biogenesis of isoprenoid precursors was shown to extend its metabolic remodeling to phenylpropanoids and lipids in addition to carotenoids, chlorophylls, and terpenoids. Such a metabolic profile was concomitant to increased colonization of the phyllosphere by the pathogenic strain <i>Pseudomonas syringae</i> pv. tomato DC3000. A thorough microbiome analysis by 16S sequencing revealed that <i>Streptomyces</i> had a reduced colonization potential in <i>chs5</i>. This study revealed that the bacteria–<i>Arabidopsis</i> interaction implies molecular processes impaired in the <i>chs5</i> mutant. Interestingly, our results revealed that the metabolic status of <i>A. thaliana</i> was crucial for the specific recruitment of <i>Streptomyces</i> into the microbiota. More generally, this study highlights specific as well as complex molecular interactions that shape the plant microbiota.