In complex Social-Ecological Systems (SES), the interplay between ecological and social components shapes trajectories that impact human well-being and ecosystem services. While SES dynamics have been studied in static conditions, there has been less attention to how said systems respond to shocks and stressors over time and space. This special issue presents a collection of articles that use diverse methodologies—ranging from system dynamics modeling to participatory approaches—to analyze past SES changes and discuss future scenarios. Case studies from regions including Brazil, Colombia, Mexico, Honduras, Chile, Ethiopia and Mongolia illustrate key variables influencing social–ecological transitions and provide insights into potential policy strategies to support sustainable SES. The studies underscore the need for multi-scalar approaches to SES research that explicitly theorize and empirically assess trajectories across space and time.