Corn (Zea mays L.) is an important crop that contributes to global food security, but understanding how farm management practices and soil health affect corn grain nutrient analysis and therefore human health is lacking. Leveraging Rodale Institute's Farming Systems Trial—a long-term field experiment established in 1981 in Kutztown, PA, USA—this study was conducted to assess the impact of different agricultural management systems on corn grain nutrient profiles in a long-term trial that has resulted in differences in soil health indicators between treatments as a result of long-term management. The main plot factor was two tillage practices (intensive and reduced) and the subplot factor was four cropping systems (non-diversified conventional [nCNV], diversified conventional [dCNV], legume-based organic [ORG-LEG], and manure-based organic [ORG-MNR]). Generally, the levels of amino acids, vitamins, and protein in corn grain were greatest in the ORG-MNR system, followed by the ORG-LEG and dCNV systems, and finally the nCNV system. It is important to consider that the observed difference between the organic and conventionally grown grain could be due to variations in corn hybrids that were used in those systems. However, nutrient composition of corn differed within cropping systems but between management practices (diversified crop rotation and cover cropping) which also contributed to differences in soil health indicators (soil compaction, soil protein, and organic C levels) that may also influence grain nutrient concentrations. With the exception of methionine, nutrient concentration in corn grain was not affected by different tillage regimes. These findings provide novel information on corn grain nutritional quality of organic and conventional cropping systems after long-term management and give insights into how system-specific components affect nutrient composition of corn grain.