Combining economic performance with environmental and social concern has been a developing topic in recent decades. Eco-efficiency analysis is a widely applied tool to assess the efficiency of agricultural systems, while increasingly considering their environmental and social impact. The main objective of this article is to accomplish a literature review on the application of eco-efficiency analysis in agricultural systems, focusing on methods and indicators that are most regarded for the quantitative assessment of agricultural eco-efficiency. The literature review found two main methods most widely applied to assess eco-efficiency: Life Cycle Assessment (LCA) and Data Envelopment Analysis (DEA), which are often combined. LCA is generally focused on the assessment of the environmental impacts of products and practices. DEA is mostly used to measure the eco-efficiency of decision-making units, such as farms, regions, or countries, and has no subjective focus on neither technical nor environmental performance. Both methods share a wide range of economic and environmental indicators but fail to incorporate the social dimension of sustainability into the eco-efficiency analysis. A simple framework, based on Data Envelopment Analysis, is offered to assess the eco-efficiency of the Brazilian agriculture, aiming at identifying the benefits and limitations of the analysis.