Sustainable fertilizer technologies are essential to address nutrient losses, environmental pollution, and inefficiencies associated with conventional urea application. In this study, humic acid–functionalized starch (St–HA) gel coatings were developed and optimized via a Wurster fluidized-bed system to produce controlled-release urea granules, with an additional carnauba wax outer layer to further extend nutrient release duration. The coating formulation was synthesized through in situ crosslinking of tapioca starch with humic acid using N,N′-methylenebisacrylamide and potassium persulfate, yielding a cohesive film. A central composite rotatable design (CCRD) was employed to investigate the influence of atomizing air pressure, fluidizing air flow rate, fluidized-bed temperature, and spray rate on coating performance. Comprehensive characterization; including FTIR, XRD, rheological analysis, thermogravimetric studies, water retention, biodegradability, and surface abrasion, confirmed chemical crosslinking, structural stability, and mechanical robustness of the coatings. Nitrogen release analysis in both water and soil demonstrated a substantial extension of release longevity from less than 2 days (uncoated) to 18–20 days for St–HA-coated urea, and up to 28 days with the additional wax coating. Coated granules exhibited low abrasion (8–24%), high water-retention capacity, and 68% biodegradation in 60 days, ensuring environmental compatibility. The findings establish St–HA/wax hybrid coatings as a viable, eco-friendly strategy for controlled-release fertilizers, integrating renewable feedstocks with scalable industrial processing for precision nutrient management.