This study aims to develop and evaluate an engineered organo-mineral composite (CCBN674) derived from bentonite, palm oil mill sludge, and shell-derived limestone for improving the physicochemical properties of tropical peat soils and enhancing soybean (Glycine max) productivity under field conditions. The material was designed as a multifunctional peat soil ameliorant with combined nutrient retention, acidity neutralization, and slow-release fertilization functions. The composite formulation was optimized based on nutrient composition and soil neutralization performance. Mineralogical and structural characterization was performed using X-ray diffraction (XRD), while surface morphology and elemental composition were analyzed using scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM–EDS). Field experiments were conducted under tropical peatland conditions with treatments including control, conventional NPK fertilization, CCBN674 application, and combined NPK + CCBN674. The results showed that the composite contained montmorillonite and other aluminosilicate phases favorable for nutrient adsorption and retention. The optimized formulation exhibited nitrogen, phosphorus, and potassium contents of 2.101%, 1.680%, and 0.125%, respectively. Application of shell-derived limestone significantly increased the pH of the formulation above 12 and improved peat soil pH from strongly acidic conditions (pH 1–3) to near-neutral levels (pH 6.8–7.5). Field results indicated that soybean plants under control and sole NPK treatments failed to survive under extreme peat acidity, whereas CCBN674 treatment supported successful plant establishment, achieving plant heights of 34.33 ± 9.91 cm, leaf numbers of 19.67 ± 5.30, and 9.23 ± 3.66 filled pods per plant. The findings suggest that the composite improves plant performance through combined effects of acidity neutralization, nutrient adsorption–desorption regulation, and enhanced rhizosphere stability. A key limitation of the study is the absence of long-term field validation and multi-season assessment of soil stability and nutrient dynamics. Nevertheless, the developed material demonstrates strong practical potential as a low-cost and sustainable peat soil amendment for tropical agriculture. The originality of this work lies in the integration of mineral, organic, and alkaline waste streams into a single engineered system with demonstrated field-scale effectiveness in extreme peat conditions.