Efficient nutrient management during the production of plug seedlings is essential for ensuring the uniformity and mechanical transplantability of onion (Allium cepa L.) seedlings cultivated in high-density 448-cell trays. However, there is a lack of evidence-based guidelines for fertilizer composition specifically designed for tray-bench nursery systems. This study assessed the effects of four commercial water-soluble fertilizers with varying N–P–K formulations (S: 25-8-16, H: 23-5-15, M20: 20-20-20, M30: 30-10-10) against an unfertilized control to identify the optimal nutrient ratios for producing high-quality plug seedlings. Fertilizers were applied biweekly, beginning 14 days after sowing, and growth characteristics along with tissue mineral contents were evaluated at 48 days. All fertilized treatments significantly outperformed the control in terms of leaf number, pseudostem diameter, root number, and fresh weight (p ≤ 0.05). Among the fertilizers, M30 (30-10-10) yielded the highest-quality seedlings, demonstrating thicker pseudostems (2.5 mm), greater fresh weight (0.85 g), and the highest root count (13.7), indicating superior suitability for mechanical transplanting. Tissue analysis revealed elevated nitrogen concentrations (1.7–2.0%) in the fertilized seedlings, which supports enhanced early biomass accumulation in peat-based media with initially low nutrient levels. These results indicate that high-nitrogen fertilizer formulations effectively promote balanced shoot and root growth, as well as robust root-ball formation in onion plug seedlings. The findings offer practical guidance for fertilizer selection in tray-bench nursery systems, contributing to improved transplant success and increased labor efficiency in mechanized onion production.