This paper synthesizes and builds on recent critiques of the resilience literature; namely that the field has largely been unsuccessful in capturing the complexity of governance processes, in particular cause–effects relationships. We demonstrate that absence of a causal model is reflected in the black-boxing of governance processes which is problematic for resilience studies with explanatory ambitions. We introduce mechanism-based thinking as alternative research perspective that offers more analytical rigour and elaborate the key principles of this approach. Mechanism-based approaches are aligned to the ways of thinking in systems theory and complexity sciences and can be used to advance scientific inquiry and policy practice to govern complex sustainability issues.