Optimizing sustainability among smallholder farms poses challenges due to inherent trade-offs. In the study of organic and conventional cocoa smallholder farming in Ghana, 398 farms are assessed using the Food and Agriculture Organsation of the United Nations (FAO) Sustainability Assessment of Food and Agriculture systems(SAFA) Guidelines and Sustainability Monitoring and Assessment Routine (SMART)-Farm Tool. Organic farming exhibited synergies in environmental aspects (e.g., soil quality, energy efficiency) and between biodiversity conservation and risk management. Conventional farming showed potential vulnerabilities, including trade-offs with long-range investments (e.g., chemical inputs) and species diversity. Both systems demand tailored approaches for short-term economic and environmental sustainability, aligning with community-wide long-term goals. To mitigate trade-offs in conventional farming, smallholders should adopt practices like material reuse, recycling, and recovery within their operations.