Cover crops can play an important role in improving the environmental sustainability of agricultural production systems. Nevertheless, adoption of the practice in the Corn Belt remains relatively low. Factors identified as major barriers to the use of cover crops by farmers in Nebraska are concerns about possible negative impacts to the commodity crop. To better understand of possible impacts and management of cover crops, we aimed to characterize how cover crops impact soil microbial communities in three locations across Nebraska. We used soybeans as a model grain crop and planted different maturity groups (MG) with a range of harvest dates from late summer to late fall. A 50:50 mixture of oats and rye were planted at harvest or remained fallow in the control treatment. Soil samples were collected during cover crop planting in fall 2017, and before cover crop termination in spring 2018. Bulk DNA was purified and 16S (V4V6) and ITS2 regions were sequenced using the Illumina Mi-Seq platform. Soil chemical properties, environmental, and agronomic variables were measured at each site. Sequence variants were obtained using dada2 plugin in QIIME2 (version 2018.8). Filtering, visualization, and comparison of microbiome data will be analyzed using phyloseq. Results will be used to determine how soybean MGs impact microbial diversity and whether this correlates with increased plant biomass and yield. Our aim is to identify microbial species that can be beneficial/antagonistic or are indicators healthy soils, high yield, or disease incidence in the commodity crops.