In the last two decades, a rich empirical knowledge base has accumulated on the complex interactions of actors, societies and ecosystems that shape the dynamics of social-ecological systems (SES), however, theoretical developments have lagged behind. A better understanding of how complex social-ecological interdependencies play out over time in different contexts can help find entry points for governance and identify ways to navigate SES onto more sustainable trajectories. In view of these gaps and needs, the MuSES project aimed to 1) assess the potential of process-relational perspectives to account for the continuously changing nature of SES and overcome the human-nature dichotomy. A shift towards a process perspective focuses attention on processes and relations, not objects, as the fundamental elements that shape the emergence of SES; 2) analyse the role of cross-scale interactions for SES's responses to change. We focused on food production systems, particularly small-scale fisheries and small-holder agriculture, and the role of relations between producers and traders as critical links connecting biophysical and social dynamics across scales. Through combining empirical research with dynamic modelling we identified how these relationships affect outcomes in different context; 3) synthesize insights from our studies, theoretical modelling and the literature to develop middle-range theories of SES change. The project contributes novel conceptualizations, frameworks and methodologies for the analysis of the dynamics of SES that focus on social-ecological interactions or relations as key explanatory factors and generalize through a process of link rich-contextual knowledge with modelling. Our research on cross-scale dynamics has highlighted the interplay of multiple social and ecological processes, such as the embeddedness of trading in social relations or the importance of social-ecological interactions for agricultural innovation, that influence SES responses to change. Based on these insights we propose a middle-range theory of small-scale production systems' responses to environmental or institutional change. The project also contributes a reflection on the types of theories and modes of theorizing that fit the complex and contested problem contexts in sustainability science, proposing novel modes of theorizing at the interface of science and society. Both insights are important contributions to governance for sustainability.