Ecological intensification is a concept based on the intensive involvement of ecological functions in order to propose new agriculture production systems. This concept is closely related to agroecological principles and to the ecosystem services framework proposed by MEA (2005). In order to drive the transition of agriculture systems there is a need for tools and methods. Emergy accounting (EA) based on the assessment of energetic flows into productive system is a good candidate to qualify ecological intensification state of agriculture systems. In order to illustrate this idea, we propose here the results of a study where EA and Life Cycle Assessment (LCA) are associated to the perception of ecosystem services (PES) by the farmers, in pond systems in France. EA and LCA give complementary results. The LCA is specifically sensitive to yields and to the inclusion of industrial inputs. In contrast, EA better reflects the inclusion of natural resources and their transformation inside the production system. Significant correlations (p<0.05) appeared between PES and few LCA impact categories and EA indicators. The sensitivity to provisioning services was positively correlated with eutrophication potential and negatively correlated with the % Renewability. The sensitivity to hydrological regulation was positively correlated with land occupation and water dependence; the sensitivity to cultural services was negatively correlated with ecosystem quality; the sensitivity to nutrient cycling service was positively correlated with ecosystem quality, water dependence and the Emergy Index of Sustainability. Most of these relations were explained by the inclusion of natural resources in the production system and by the relative attention paid by farmers to provisioning services vs. support, regulation and cultural services. This study shows the agreements between Emergy accounting and ecosystem services perception and therefore its relevance in the qualification of ecological intensification status especially in agricultural systems closely associated with natural ecosystems