Archetype analysis is a key tool in landscape and sustainability research to organize social-ecological complexity and to identify social-ecological systems (SESs). While inductive archetype analysis can characterize the diversity of SESs within a region, deductively derived archetypes have greater interpretative power to compare across regions. Here, we developed a novel archetype approach that combines the strengths of both perspectives. We applied inductive clustering to an integrative dataset to map 15 typical SESs for 2016 and 12 social-ecological changes (1999–2016) in Andalusia region (Spain). We linked these types to deductive types of human-nature connectedness, resulting in a nested archetype classification. Our analyses revealed combinations of typical SESs and social-ecological changes that shape them, such as agricultural intensification and peri-urbanization in agricultural SESs, declining agriculture in natural SESs or population de-concentration (counter-urbanization) in urban SESs. Likewise, we identified a gradient of human-nature connectedness across SESs and typical social-ecological changes fostering this gradient. This allowed us to map areas that face specific sustainability challenges linked to ongoing regime shifts (e.g., from rural to urbanized systems) and trajectories towards social-ecological traps (e.g., cropland intensification in drylands) associated with decreasing human-nature connectedness. This provides spatial templates for targeting policy responses related to the sustainable intensification of agricultural systems, the disappearance of traditional cropping systems and abandonment of rural lands, or the reconnection of urban population with the local environment, among others. Generally, our approach allows for different levels of abstraction, keeping regional context-specificity while linking to globally recognisable archetypes, and thus to generalization and theory-building efforts.