Although corn is the most important and nitrogen (N)-fertilized crop, there is a lack of long-term data on the effects of organic and inorganic N fertilizers on the N balance and losses for corn systems under different tillage approaches. From 2012 to 2023, we assessed the effects of the N source on the grain yields from cultivated continuous corn receiving irrigation at a site with minimal erosion in Fort Collins, Colorado, USA, and compared these effects to no-till (NT) and strip till (ST) systems receiving inorganic N. An N balance accounting for N and carbon (C) sequestration found a system nitrogen use efficiency (NUESys) for organic N fertilizer (manure) with a tillage of 86.6%, which was higher than the NUESys of 62.6% with inorganic N fertilizer (enhanced efficiency fertilizer, EEF). Conventional tillage with manure use is a good management practice that contributed to higher grain yields (2 of 11 years), C sequestration (p < 0.05), soil organic N content (p < 0.05), and soil phosphorus (P) content than inorganic N fertilizer with tillage (p < 0.05). The tilled systems, whether receiving organic or inorganic N fertilizer, had higher yields and grain N content than the NT and ST systems receiving inorganic N fertilizer (p < 0.05). The grain production of the cultivated system receiving organic N fertilizer did not decrease with time, while the yields of the cultivated system receiving inorganic N fertilizer decreased with time (p < 0.05), suggesting that cultivated systems receiving organic N fertilizer may be more sustainable and better able to adapt to a changing climate. Additionally, a combination of manure (30% of N input) with EEF (70% of N input) contributed to a synergistic effect that increased the agronomic productivity (harvested grain yields).