Agricultural stakeholders disagree on how to put the general concept of sustainability into practice. But most recognize the need for assessment methods to characterize the current situation and gauge progress yet to be made. Many sustainability assessment methods for agricultural systems have been published, but very few integrate ecosystem services (ES). And yet, ES indicators are key to better integrating biological processes to support the agroecological transition. Although researchers have attempted to link the concept of environmental impact (EI) and ES through life cycle analysis (LCA), gaps remain when it comes to doing so within a sustainability assessment method. Here a new method based on an original conceptual indicator framework embedding new predictive indicators of EI and ES indicators was developed. This framework covers 22 environmental themes and integrates few basic economic and social indicators. The method was implemented on 33 farms with different certifications and production specifications. All farms were members of an agricultural cooperative in north-eastern France. We selected 250 plots to cover the farms’ crop rotations. The correlation analysis showed no systemic trade-off between EI or ES and economic indicators. Meanwhile, the joint assessment of ES and EI (like the multivariate analysis), delivered more nuanced results than a classical opposition between intensive and organic farming. Some farms with a moderate or even good level of ES often do not leverage them, as shown by their high EI. The principle component analysis and subsequent hierarchical ascendant classification allowed us to distinguish five clusters providing a more complex picture than simply opposing conventional and organic agriculture. Finally, the positive deviance analysis revealed that economic, environmental and social considerations can be balanced in a way that seems to be more sustainable than, for example, an organic farm that has very successfully reduced EI but at a cost of several economic and social trade-offs.