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While soils are diverse microbial environments, only select and consistent sets of microbial taxa colonize within the endophytic compartment (EC) of root tissue, suggesting microbes in the EC pass through several levels of selection. Massive parallel sequencing of the 16S rRNA gene to profile root-associated bacterial communities of a number of <i>Arabidopsis thaliana</i> mutants allowed characterization of multiple selection mechanisms used by the plant immune system to influence EC microbiome. Specifically, the EC root microbiome of plants lacking specific pattern recognition receptors (PRRs) or NOD-like receptor (NLR) signaling components indicated that microbial perception is important for limiting EC bacterial colonization. In a parallel survey with <i>A. thaliana</i> mutants in defense phytohormone biosynthesis and/or downstream signaling, we discovered that SA in particular plays a significant role in EC microbiome membership. These findings were confirmed when wildtype and mutant plants were inoculated with a well-defined mixture of bacterial root isolates and treated half of the plants with exogenous SA, allowing us to untangle direct SA effects from plant-dependent effects on bacterial communities. Together, these studies describe specific functions of multiple components of the plant immune system to shape EC microbiome composition, offering an exciting new context for how plant immunity promotes homeostasis and health.