Maize (Zea mays L.) is among the three most important food crops worldwide. Maize growth is affected by high aluminium content in acid soils, which constitute nearly 50% of the world’s cultivable area. Therefore, the cultivation of aluminium-tolerant maize hybrids could be a healthier alternative and an attractive food source in these regions. In this regard, to produce hybrids kernels, 16 inbred lines aluminium-tolerant (Al-T) and aluminium-susceptible (Al-S) maize were screened for their constitutive patterns of selected nutrients and phytochemicals. Proximate analysis, free phenolic acids (FPA) and cell wall-bound phenolic acids (CPA) contents, as well as antioxidant capacity (AOX) were assayed in the anatomical kernel parts (pericarp, endosperm, and germ). Kernels of Al-T maize contained significantly higher germ protein, oil, and fibre (2.9, 3.0, and 0.5%, respectively) than Al-S kernels (1.9, 1.8, and 0.3%, respectively). Importantly, the nutraceutical contents in terms of pericarp FPA and germ CPA were significantly higher in kernels belonging to Al-T maize (92 mg and 140 mg EGA/100 g). The highest AOX was observed in germ CPA of Al-T kernels (9.0 mmol TE/100 g). The results herein indicate that Al-tolerance mechanisms induce positive changes in the nutrients and phytochemicals; this implies that the hybrids generated using Al-T maize inbred lines could emerge as an attractive source of nutrients and phytochemicals in farming regions containing acid soils.