Energy and environmental issues have been high on agendas of European Union members since they are intertwined with efforts to mitigate climate change and expand the economy. We intend to analyze the energy and environmental efficiency of EU countries using enhanced data envelopment analysis techniques. First, our study investigates energy efficiencies using the bootstrap DEA technique, which addresses the problem of statistical noise. Further, we examine the environmental and eco-innovation efficiency of EU countries by employing the two-stage superslack-based DEA technique, which is one of the most suitable approaches for modeling undesired output. According to the environmental efficiency findings, the Nordic countries are primarily more efficient whereas, in terms of eco-innovation efficiency, Germany is ranked as the top-performing country. In addition, substantial prospects for improvements exist in the efficiency of the EU countries We may conclude that this research will help policymakers in this area.