Changes in agriculture during the twentieth century led to high levels of food production based on increasing inputs and specialization of farms and agricultural regions. To address negative externalities of these changes, two forms of ecological modernization of agriculture are promoted: “weak” ecological modernization, mainly based on increasing input efficiency through crop and animal monitoring and nutrient recycling, and “strong” ecological modernization, based on increasing agrobiodiversity at different space and time scales and within or among farms to develop ecosystem services and in turn reduce industrial inputs even more. Because characterizing the sustainability of these two forms of ecological modernization remains an issue, we review the literature on livestock systems to compare their advantages and drawbacks. After defining the livestock system as a local social–ecological system embedded in a complex multi-level and multi-domain system, we characterize the two forms of ecological modernization (weak vs. strong). When sustainability is defined as a state that should be maintained at a certain level and assessed through a set of indicators (environmental, economic, and social), we highlight that one ecological modernization form might have an advantage for certain sustainability criteria, but a disadvantage for others. When sustainability is viewed as a process (resilience), we find that these two forms of ecological modernization are based on different properties: governance of the entire agri-food chain for weak ecological modernization versus local governance of agriculture and its biophysical and social diversity and connectivity, and management of slow variables for strong ecological modernization. The relevance of this sustainability-analysis approach is illustrated by considering different types of dairy livestock systems, organic agriculture and integrated crop–livestock systems.