Body of Abstract: Tropospheric ozone is a harmful greenhouse gas (GHG) to human and plant health. The effects of ozone on decreasing photosynthetic carbon sequestration and increasing oxidative stress lead to plant growth defects, reducing crop yield. Global relative yield losses range from 6-16%, 7-12%, 3-4%, and 3-5% for soybean, wheat, rice, and maize, respectively, all of which accounted for global economic losses of $14-26 billion in 2000. While humankind works toward long-term mitigation of global GHG emissions, there is an urgency to enhance the knowledge of plant responses to ozone pollution. In contrast with established knowledge of ozone impacts on above-ground tissues, roots interacting with soil microbes and absorbing nutrients to support plant fitness have been thus far overlooked. To better assess the impact of ozone on below-ground ecosystems, this study used two soybean (Glycine max) genotypes—Fiskeby III (ozone tolerant) and Fiskeby 840-7-3 (ozone sensitive) grown under elevated ozone (eOZ) in a field-based air exclusion system (AES)—to investigate plant morphological and proteomic profiles, as well as root-associated soil microbial diversity and networks. Our results showed that effects of ozone on root performance occurred prior to any growth damage in above-ground organs. However, season-long eOZ ultimately caused a 29% seed-yield reduction in Fiskeby III but a 50% reduction in Fiskeby 840-7-3. Root proteomic analysis showed changes in the abundance of proteins involved in carbon and nitrogen metabolisms, secondary metabolite biosynthesis, and stress response pathways under eOZ. Lacking carbon resources in below-ground systems under eOZ, fungal diversity and network complexity were significantly decreased, whereas bacterial diversity was more ozone tolerant. Additionally, our study identified nitrifying bacterial and diazotrophic communities were increased under eOZ. These fundings suggested that root performance and interactions with soil microbes may support nutrient acquisition to leverage ozone adaptation.