Conventional fertilization practices can lead to many ecological problems, such as nutrient imbalance, soil acidity, and reduced soil fertility, in natural rubber plantations. To address these challenges, a field investigation was strategically carried out to substitute inorganic fertilizer with organic fertilizer, consisting of six treatments: no fertilization (CK), inorganic fertilizer (NPK), 25% replacement of inorganic through organic (25% manure (M)), 50% replacement of inorganic through organic (50% manure (M)), 75% replacement of inorganic through organic (75% manure (M)), and 100% organic fertilizer (100% manure). The soil physicochemical properties (soil organic carbon (SOC), total nitrogen (TN), mineral nitrogen (N), ammonium nitrogen (NH4+-N), and nitrate nitrogen (NO3−-N)), C:N, pH, and the carbon- and nitrogen-converting enzymes β-1,4-glucosidase (BG), N-acetylglucosaminidase (NAG) and L-leucine aminopeptidase (LAP) were all determined. The partial substitution of inorganic fertilizer with organic fertilizer (i.e., 75% M at surface soil layer) showed higher SOC (14.52 g·kg−1), TN (1.06 g·kg−1), N (20.07 mg·kg−1), C:N (14.63), NH4+-N (10.63 mg·kg−1), and NO3−-N (11.06 mg·kg−1) than NPK and CK. This increase in physicochemical properties after partial replacement of inorganic with organic fertilizer resulted from higher carbon and nitrogen enzyme activities (BG (143.17·nmol·g−1·h−1), NAG (153.96 nmol·g−1·h−1), and LAP (153.48 nmol·g−1·h−1)) compared to NPK and CK. Further, the Pearson correlation and redundancy analysis (RDA) analyses confirmed a significant positive correlation between SOC, N, and soil enzymes. This study presents a new strategy for assessing the impact of partially replacing inorganic fertilizer with organic fertilizer in rubber plantations in tropical regions, mainly by modifying the soil nutrient composition.
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