Achieving ultra-low-sulfur diesel is a crucial objective in modern fuel refining, driven by increasingly stringent environmental regulations. This study presents the development of a highly efficient oxidative–adsorptive desulfurization process utilizing a nanocatalyst synthesized from biowaste eggshell-extracted calcite. The oxidation reaction was conducted in a digital basket reactor (DBR), an advanced reactor system designed to enhance mass transfer and catalytic efficiency. To further augment the catalyst’s performance, the calcite was modified with eco-friendly MnO₂, while activated carbon was employed as an adsorbent to effectively capture oxidized sulfur compounds, ensuring compliance with ultra-low-sulfur fuel standards. The synthesized nanocatalyst underwent comprehensive physicochemical characterization using SEM, EDX, BET, and FTIR, confirming its high surface area, structural integrity, and superior catalytic activity. The MnO₂/P–calcite catalyst achieved a sulfur removal efficiency of 96.5% at 90 °C, 80 min, and 600 rpm, demonstrating excellent oxidative–adsorptive performance for real diesel fuel. The integration of this innovative nanocatalyst with the DBR system presents a sustainable, cost-effective, and industrially viable approach for deep desulfurization, offering significant advancements in clean fuel production and environmental sustainability.