Modern agricultural systems rely on inorganic nitrogen (N) fertilization to enhance crop yields, but its overuse may negatively impact soil properties. Soil properties to a depth of 90 cm were studied after 36 years of inorganic N fertilization at successive rates of 0, 202, and 269 kg N ha−1 (N0, N202, and N269) in continuous corn production [Zea mays L.] (CCC), and the corn (Cs) and soybean [Glycine max (L.) Merr.] (Sc) phases of a corn-soybean (CS) rotation. Experimental plots were arranged as a split-plot in a randomized complete block design with three replications. High levels of N fertilization under CCC acidified the topsoil (N0 pH 6.6 vs. N269 pH 4.9), and increased the nitrate level eight-fold compared to unfertilized controls. Under CCC, N0 had more than twice the available phosphorus level (P) and 40% more potassium (K) than the fertilized soils. Though treatments did not impact the soil organic carbon (SOC) content, water aggregate stability (WAS) decreased during the soybean phase of the rotated treatment (Sc) when compared to CCC. Fertilization affected soil bulk density (BD), which decreased by 5% from N0 to N269 across rotations. Averaged since the start of the study, corn yields increased by 60% with N fertilizer use compared to the unfertilized controls (N0). The corn grain yield benefited from the rotation with soybeans rendering 17% more grain yield in Cs than in CCC. Yet this benefit rose to 45% more grain yield on average, when no N fertilizer was used in Cs. Our results showed that there are important trade-offs with N fertilization and long-term use of corn monocultures, as its long-term use, even in the fertile and resilient soils on the Midwestern U.S., has led to P and K depletion, soil acidification, and potentially exacerbated N losses to the environment.