Maize (Zea mays L.) yields have advanced through breeding complemented with evolving management technologies including plant density (PD) and macronutrient fertilizer inputs. Little is known about management-induced changes in plant uptake or allocation of nutrients other than macronutrients. Therefore, impacts of both PD and N rate at three levels (low, medium, and high) on Ca, Mg, and micronutrient partitioning (for pertinent plant organs at six growth stages) were investigated at four environments in Indiana. Grain Ca, Mg, Fe, and Zn contents at maturity were primarily influenced by N rate, while the PD × N rate interaction influenced those of Mn and Cu. At the whole-plant scale, PD and N rate significantly influenced all nutrient contents, and vegetative-stage nutrient accumulation averaged 91% (Ca), 51% (Fe), 47% (Zn), and 73% (Mn, Mg, and Cu) of corresponding nutrient contents at maturity. During the vegetative phase, three modes of leaf vs. stem nutrient partitioning were: (i) preferential allocation of Mg and Zn to stems; (ii) preferential allocation of Fe and Ca to leaves; and (iii) isometric partitioning of Cu and Mn. Isometric nutrient concentration patterns between Mg and Zn were documented in leaf, stem (vegetative phase), and ear (reproductive phase). Early-reproductive-stage nutrient partitioning from plant to ear was greatest for Zn and Mg and mirrored their respective harvest indices (HIs) at maturity. Nutrient HIs, concentrations (grain + stover), and internal efficiencies at maturity were positively impacted by N rate but negatively by PD. Reliable micronutrient requirement estimations for maize under diverse management and yield levels help inform future balanced-nutrient input decisions.