Sappanwood (Caesalpinia sappan L.) is a valuable plant used in natural medicine, beverages, and dyes due to its bioactive compounds, particularly brazilin. This study examined the environmental and metabolite characteristics of C. sappan collected from four regions in Indonesia: Sumedang (SMD), Majalengka (MJK), Garut (GRT), and Purwodadi (PWD). Results indicated that environmental factors, such as light intensity and altitude, varied among locations and influenced metabolite synthesis, along with differences in soil chemical properties. GRT exhibited the highest nitrogen (0.22%) and organic carbon content (2.18%), while MJK and PWD showed lower levels. Secondary metabolite analysis revealed that GRT had the highest phenolic content (33.12 mg/g GAE), flavonoid content (13.76 mg/g QE), and antioxidant activity (80.32%). Brazilin content was also highest in GRT (0.0186 mg/g) and showed strong positive correlations with total phenolics, flavonoids, and antioxidant activity, underscoring its role in oxidative stress defense. Overall, this study highlights the environmental and biochemical determinants of brazilin biosynthesis in C. sappan, offering insights for optimizing its production through targeted agronomic management and breeding strategies. The findings are valuable for advancing value-added applications of sappanwood in natural medicine and the antioxidant industry.