This study presents a comprehensive heat transfer and energy–exergy analysis of an integrated anaerobic digestion–Sabatier system for renewable methane production. The proposed configuration combines biologically optimized methane generation through mesophilic anaerobic digestion with electrochemical upgrading via modular Sabatier methanation. Thermal regulation of the anaerobic digester plays a key role in maintaining stable microbial activity and improving methane productivity under decentralized operating conditions. The anaerobic digestion unit operated at 35°C with a hydraulic retention time of 20 days, achieving methane concentrations of 60–65%. Incorporating water-assisted enhancement improved substrate–microorganism interaction and increased methane yield by approximately 30.5% compared with conventional digestion. Energy analysis demonstrated that biological methane production exhibits relatively low specific energy consumption, whereas the Sabatier upgrading pathway is strongly influenced by the high energy demand associated with hydrogen production. Exergy analysis revealed that the biological pathway experiences lower exergy destruction due to moderate temperature operation and reduced auxiliary energy requirements. In contrast, electrochemical upgrading introduces significant thermodynamic losses primarily related to upstream hydrogen generation. The integrated system achieved an estimated 42% reduction in CO₂-equivalent emissions compared with uncontrolled methane release scenarios. The results indicate that biologically optimized anaerobic digestion provides the most energy-efficient pathway for decentralized renewable methane systems, while Sabatier upgrading can serve as a complementary option under conditions of surplus renewable electricity. The proposed framework highlights the importance of heat transfer management and thermodynamic optimization for improving the performance and sustainability of waste-to-energy technologies.