Purpose While distinct soil microbiomes and individual soil microbial taxa can alter particular plant traits under highly controlled conditions, little is known about the role of particular microbial taxa and microbial functions within complex soil microbial communities for mediating plant phenotypes or if the strength of microbial mediation of plant phenotype varies among plant species or plant phenotypic traits. Examining how the plant phenotype spectrum is influenced by the taxonomic and functional composition of complex soil microbial communities allows for a more accurate understanding of the biotic environmental drivers of plant phenotype. Methods Using rhizosphere soil collected from field sites, we conducted a microbiome transfer glasshouse experiment to test the hypothesis that the taxonomic and functional composition of different soil microbiomes would differentially shift growth, physiological or reproductive phenotypes of three Solidago species. Results We found that soil microbiome inoculations influenced Solidago growth traits more than physiological and reproductive traits. We found that root growth of one of the Solidago species was negatively correlated with 77% of the indicator bacterial and fungal taxa from one of the soil microbiome treatments. Conclusions Soil microbial mediation of plant phenotype varies by plant traits, is not universal across plant species, and can be associated with a small number of microbial taxa. This study illustrates that specific microbial taxa within a soil microbiome are associated with shifts in plant phenotype by pinpointing important individual microbial taxa from complex field soil microbial communities.