Onion (Allium cepa) is one of the world’s most consumed, nutrient-dense foods, low in calories and containing a rich amount of major bioactive compounds, vitamins, and minerals. The purpose of this study was to determine the influence of different nitrogen (N) fertilizer sources on the nutritional and phytochemical qualities of short-day onions. A white-type onion (cv. Texas Grano) was subjected to different fertilizer application treatments, namely (i) pre-plant base application of 80 kg ha−1 N from CaCN2, alone or in combination with (ii) top-dressing with 50 kg ha−1 N from limestone ammonium nitrate (LAN), or (iii) top-dressing with 50 kg ha−1 N from urea, (iv) pre-plant base application of 80 kg ha−1 N from LAN and top-dressing with 50 kg ha−1 N from LAN, (v) pre-plant base application of 80 kg ha−1 N from urea and top-dressing with 50 kg ha−1 N from urea, and (vi) 0 kg ha−1 N. Pre-plant application of CaCN2 (80 kg ha−1 N) outperformed standard onion fertilizers, urea (130 kg ha−1 N) and LAN (130 kg ha−1 N), significantly enhancing total phenolic content, antioxidant activity, and calcium (Ca) and potassium (K) content in onion bulbs. Applying 50 kg ha−1 N from urea as top-dressing with the pre-plant application of CaCN2 (80 kg ha−1 N) elevated total phenolics (5.48 mg GAE g−1) and flavonoids (0.741 mg CE g−1) in the onion bulbs. The highest antioxidant activity (55.9%) and free radical scavenging activity (26.3%) were achieved with top-dressing 50 kg ha−1 N from LAN following CaCN2 pre-plant application. Application of CaCN2 + urea also significantly increased onion bulb potassium (2335 mg kg−1) and calcium (828 mg kg−1) contents, while CaCN2 combined with LAN improved magnesium (123.3 mg kg−1) content. This study recommends pre-plant CaCN2, top-dressed with either LAN or urea, for improved phytochemical components, antioxidant activities, and certain mineral content in onion bulbs. These findings present a practical approach for cultivating nutrient-rich and phytochemically abundant onion bulbs, promoting improved human health.