The accumulation of agricultural waste poses significant agronomic and environmental challenges in tropical smallholder farming systems where organic wastes are still underutilized. This study evaluated the effectiveness of vermicomposting with Eisenia fetida to enhance nutrient recovery and the quality of organic fertilizers generated from agricultural waste. Four substrate treatments—cow dung, chicken manure, and vegetable waste (T2), cow dung and vegetable waste (T3), poultry manure and vegetable waste (T1), and a control group free of earthworms (T4)—were assessed during 60 days. Bulk density, pH, electrical conductivity, organic carbon, total nitrogen, accessible phosphorus and potassium, and the C: N ratio were among the significant physicochemical properties that were investigated. Vermicomposting significantly increased the nutritional content; the C: N ratio decreased from 26.43 (control) to 12.23, suggesting improved compost maturity, and T2 contained the greatest quantities of potassium (1.45%), phosphorus (1.21%), and total nitrogen (2.63%). Another sign of improved mineralization efficiency was a significant decrease in organic carbon during the decomposition phase. Vermicomposting improved nutrient availability, compost maturity, and structural quality in comparison to traditional composting. These results show that vermicomposting is a successful resource recovery technique that increases nutrient availability, improves resource efficiency, supports sustainable and climate-resilient agricultural systems, and turns agricultural waste into useful organic fertilizer.