Numerous studies have reported that most biotic and abiotic factors alter soil microbiome composition, and these changes range from small (e.g., 3%) to large (e.g., 30%). Plants directly interact with soils and their microbiomes to gain water, nutrients, and stabilize themselves. Yet we have little understanding of how much change in a soil microbiome is likely to impact plant traits and functions. This is an important gap for two reasons: 1) are small changes in microbiome composition biologically relevant? And 2) can we manipulate soil microbiomes to alter plant traits and function? We set out to address this question in a greenhouse experiment in tomato. We extracted a diverse microbial community from restored prairie soil, exposed it to five levels of antibiotics, fungicides, or both, and added the manipulated communities to tomatoes growing in sterile soil. We then characterized microbial community composition in soil, roots, and leaves and measured a suite of plant and fitness traits (height, leaf length, leaf width, leaf number, fruit number, SPAD, above and belowground biomass, and fruit biomass) to determine whether changes in soil microbiome composition influenced plant traits. First, we found that the application of antibiotics or fungicides, but not the level of application of antibiotics or fungicides impacted soil community composition and all plant traits. Thus, we were able to document the influence of an overall change in community composition on plant traits, but not levels of changes in community composition. Second, we found clear signatures of changes on community composition on traits important for plant fitness and agriculture: flower and fruit number. Third, we have linked changes in soil microbial community composition to changes in the microbial composition of other plant compartments (e.g., roots and leaves). As a result we have clearly identified that changes in soil microbial community composition can impact key plant traits, however what proportion of change in microbial community composition results in changes in key plant traits remains an important question for research in the future of soil biodiversity.