Declining nutrient densities of crops in the past 50–70 years have been attributed to unsound agricultural practices and plant breeding focus on yield rather than quality. Few studies have quantified the soil and nutritional quality of grains in organic and conventional farms and reported results are scarce and inconsistent. The Rodale Institute's Farming Systems Trial (FST) was established in 1981 to quantify the effects of long-term organic and conventional grain cropping systems and tillage practices. A 2014 study to quantify effects on the nutrient density of oat grains was integrated into three systems within the long-term trial: organic manure-based (MNR), organic legume-based (LEG), and conventional synthetic input-based (CNV), split between tilled (T) and no-till (NT) practices. Oat grains with hulls removed were analyzed for minerals (n = 24), vitamins (n = 24), amino acids (n = 24) and proteins (n = 24), while soil samples to a depth of 10 cm were analyzed for elemental minerals, and total carbon (C), nitrogen (N) and sulfur (S). Organic systems increased six out ten soil minerals whose concentrations were influenced by cropping systems: aluminum (Al), iron (Fe), chromium (Cr), calcium (Ca), barium (B) and strontium (Sr). All essential amino acids were greater in oat grains under LEG systems compared with other systems except lysine, histidine and methionine. Both LEG systems also increased 12 out of 13 non-essential amino acids in oat grains. Total oat N, C and S required for amino acid synthesis tended to be greater in organic systems. Soil N, C and S were highly correlated with total oat amino acids under organic systems compared to CNV. Organic LEG had significantly greater vitamin B1 than MNR and CNV. These results suggest that nutrient concentrations of oat grains were greater in organic systems compared to CNV systems, and the increase could be partially explained by the long-term soil management differences between the systems.