Over the recent decades, the evolution of the European Union (EU) agricultural system has resulted in significant structural changes in member states. Knowledge about the nature and main patterns of structural change is critical to select a sustainable development path for the EU agriculture. This paper contributes to the academic discourse on structural changes in agriculture demonstrating the nexus between socioeconomic and environmental aspects of development. In this regard, results are important to understand the contribution of the EU agriculture to climate change, because study deals with energy use and greenhouse gas emissions. The research covers period from 2008 to 2018 and investigates the fundamental structural change measures, namely, gross value added, labour and agriculture-related energy emissions, in EU member states. Structural changes are investigated applying a shift-share analysis that allows calculating a performance of individual member states, compared to the EU economy. The applied shift-share model investigates the situation of individual member states employing three components. The first component tracks the development of the selected measures with the EU economy growth, the second component shows the change due to effect of economic activities and the third shows competitiveness of agriculture in member states. The shift-share analysis empowers ranking member states in accordance with their progress towards the sustainable development. Findings suggest that EU economy faces the outflow of labour from agriculture and this trend is common for most countries. The changes of gross value added and emissions for fuel combustion demonstrate both upward and downward trends. However, research results suggest that new member states often face more fundamental changes.