<p>Indragiri Hilir is one of the primary coconut production centers in Indonesia, contributing approximately 11.39% of the national total, with an annual production volume of around 300,000 tons. This prominence has been shaped by the region’s long-standing history as a coconut hub for centuries. However, the dominance of peatland, covering 85% of the total area, presents significant challenges, particularly for the 98.95% of smallholder farmers managing these plantations. Peatland landscapes create geographical fragmentation, with river-dominated access limiting mobility and increasing transportation costs. Consequently, smallholder farmers, particularly in post-harvest supply chains, rely on actors with greater resource control. To capture the complexities of the coconut supply chain, this study uses a socio-ecological framework, acknowledging the system’s adaptability and interconnections. This framework highlights sustainability challenges arising from dynamic interactions and feedback loops between human activities and ecological conditions. Conducted across eight districts in Indragiri Hilir—Pulau Burung, Kateman, Teluk Belengkong, Pelangiran, Enok, Tanah Merah, Batang Tuaka, and Reteh—this qualitative in-depth interview study involved 75 informants engaged in the coconut supply chain, primarily farmers and middlemen. The findings reveal the emergence of new subsystems shaped by socio-economic and ecological adaptations, including strong connection with middlemen, industrial collecting points as innovations, local labor rotation on plantations, fairness in coconut weighing methods, farmers’ autonomy in selling their harvests, and collaborative initiatives in coconut agriculture on peatland. The study further emphasizes that balancing stakeholder interests beyond mere economic gains is essential for ensuring the long-term sustainability of the ecosystem.</p>