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To understand factors that influence the assembly of microbial communities, we inoculatedMedicago sativawith a series of nested bacterial synthetic communities and grew plants in distinct nitrogen concentrations. Two isolates in our eight‐member synthetic community,Williamsiasp. R60 andPantoeasp. R4, consistently dominate community structure across nitrogen regimes. WhilePantoeasp. R4 consistently colonizes plants to a higher degree compared to the other six organisms across each community and each nutrient level,Williamsiasp. R60 exhibits nutrient specific colonization differences.Williamsiasp. R60 is more abundant in plants grown at higher nitrogen concentrations, but exhibits the opposite trend when no plant is present, indicating plant‐driven influence over colonization. Our research discovered unique, repeatable colonization phenotypes for individual microbes during plant microbiome assembly, and identified alterations caused by the host plant, microbes, and available nutrients.