Winter annual cover crops can be planted before soybean in Mississippi for many agronomic reasons. Incorporating winter annual cover crops into soybean production changes the seasonal hosts within fields. Some studies suggest that reducing tillage and using diverse species of cover crops can increase arthropod diversity and predator activity. Neonicotinoid seed treatments are often implemented to combat early season insect pests in soybean that follow cover crops, but negative effects on the environment such as reductions in biodiversity are often attributed to these compounds. We conducted an experiment to measure the effects on the diversity of the soybean epigeal and foliar communities when incorporating cover crops as well as insecticidal seed treatments into Mississippi soybean growing systems. Our results showed that legume cover crops had significant impacts on the epigeal community diversity of soybean planted behind them. These cover crops, especially hairy vetch, supported a more diverse foliar community before termination. To prevent increases in herbivorous arthropods, neonicotinoid seed treatments can be used without affecting epigeal predators such as beetles, ants, and spiders. The neonicotinoid seed treatments affected arthropod diversity, but the reductions were mainly caused by decreases in herbivorous pest insects that fed on treated soybean plants.