Coffee is an important agricultural commodity that is branded according to its environmental criteria in the global market. Therefore, Indonesia’s coffee production system needs to be investigated to meet the demand for eco-labeling, which has become a consumer preference. This study aims to assess the comprehensive sustainability evaluation of coffee production nurtured by an organic fertilizing system (OFS), chemical-organic fertilizing system (COFS), and chemical fertilizing system (CFS) that focuses on the energy–environment–economic nexus. A life cycle assessment (LCA), life cycle cost analysis (LCC), and energy analysis were performed as methods to evaluate the environmental impact, economic performance, and energy requirement analysis. The results indicated that the OFS had superior performance in two sustainability aspects: resulting in the lowest environmental damage and generating the highest economic benefit. Simultaneously, COFS shows the highest sustainability performance as it consumes the least energy. In contrast, CFS indicated the lowest sustainability performance in all aspects: highest environmental impact, lowest economic benefit, and highest energy consumption. Therefore, OFS is strongly recommended to be applied broadly, considering its environmental and economic superiority. Consequently, massive OFS application was followed by higher energy consumption. Alternatively, COFS can be considered for application due to its higher energy performance, even though it can potentially result in higher environmental damage and lower economic benefit. However, the government should explicitly provide some effort for the broad application of OFS in financial and assistance support since the shifting process needs more time to adapt.