Corn (Zea mays L.) is a commonly grown crop with high nitrogen (N) demand. Modern hybrids and intensive fertilization practices have increased yields but may have compromised below-ground traits, such as root growth and biological soil health. Newly introduced short-stature corn hybrids are recognized for their lodging resistance; however, limited information is available regarding their belowground benefits. This study aimed to investigate how fertilization rates affect the belowground performance of short-stature corn compared to conventional tall-stature corn hybrids. Field experiments were conducted at two locations in Indiana, encompassing two contrasting corn statures and four nitrogen (N) rates (0, 100, 200, and 300 kg/ha). Root and soil samples were collected at a depth of 0-120 cm during the corn R2 growth stage using a hydraulic Giddings probe, followed by scanning and image analysis to quantify both belowground and aboveground biomass. Root biomass and length in short-stature corn were 1.35 and 1.42 times higher, respectively, compared to tall-stature corn, with greater differences observed in soils with higher organic matter content. Across both soil types, root biomass and length peaked at 200 kg/ha of nitrogen, with the majority concentrated in the top 30 cm layer. Soil microbial biomass, POXC, and PMC levels increased in high-organic-matter soil, but were unaffected by corn hybrids and nitrogen addition. This study demonstrates that short-stature corn hybrids exhibit enhanced root biomass and length, particularly under optimal N fertilization, while soil biological indicators are largely unaffected by hybrid type or N rate. Therefore, these findings emphasize the importance of optimizing nitrogen rates with short-stature hybrids to enhance root traits and soil health, guiding sustainable crop management decisions.