Significance The composition of bacterial populations in the human digestive tract is known to affect our well-being, to influence our ability to overcome diseases, and to be tightly linked with the host genotype. In contrast, the extent to which variation in the plant genotype affects the associated bacteria and, hence, plant health and productivity remains unknown, particularly of field-grown plants. Genetically modified poplars, down-regulated for cinnamoyl-CoA reductase, substantially influence the microbiome of the plant endosphere without perceptible impact on the rhizosphere microbiota. Unraveling the host genotype-dependent plant–microbe associations is crucial to comprehend the effects of engineering the plant metabolic pathway and possibly to exploit the eukaryote–prokaryote associations in phytoremediation applications, sustainable crop production, and the production of secondary metabolites.