Robusta coffee cultivation in Malinau Regency has been increasingly associated with forest land conversion, thereby intensifying the need for sustainable management practices that align with both environmental conservation and rural livelihood enhancement. To evaluate the sustainability of Robusta coffee farming systems, the sustainable livelihood framework was applied, focusing on five key livelihood capitals: natural, human, social, physical, and financial. A mixed-methods approach involving Multidimensional Scaling (MDS) and thematic analysis was employed to quantify sustainability levels and identify leverage points for strategic intervention. Results indicated that most capitals were classified as either “unsustainable” or “less sustainable.” Social capital demonstrated the lowest performance, with an index of 15.10, while financial capital followed at 20.88; both were categorized as “unsustainable.” Natural capital (26.13) and human capital (26.09) were deemed “less sustainable,” whereas physical capital showed relatively higher resilience with an index of 46.61, though still within the “less sustainable” threshold. Key constraints included insecure land tenure, underdeveloped infrastructure, limited social cohesion, and economic dependence on non-coffee income sources. Strategic interventions were proposed, including the certification of land ownership for 70% of coffee farmers within three years, the revitalization of farmer cooperatives to improve social capital, and the enhancement of rural infrastructure, particularly targeting 85% electricity coverage in coffee-producing areas by the second year. The integration of Geographical Indication (GI) certification with agroforestry-based production systems was identified as a pivotal strategy to reconcile ecological integrity with market competitiveness. By year four, price premiums of up to 40% in domestic markets and 60% in international markets were targeted through value addition and branding. These integrated measures are expected to reinforce livelihood resilience while promoting long-term socio-ecological sustainability in Malinau’s coffee landscapes.