Emergy analysis has become a widely used tool for comprehensively assessing systems, offering valuable insights into their environmental and economic sustainability. This study employs a bibliometric analysis, between the years 2000 to 2022, to explore the advancements in evaluating agricultural systems using emergy and identify the primary challenges in this field. The analysis reveals a growing annual scientific production, with prominent journals, as determined by their Impact Factors, publishing a substantial number of these assessments. Furthermore, the study delves into the analysis of emergy indicators across various agricultural production systems, including crop, livestock, and integrated crop-livestock (mixed) systems. The findings demonstrate the efficacy of these indicators in distinguishing the sustainability of different production types. These results not only inform researchers about critical considerations to be taken into account but also provide an overview of the current state of research in this field.