Ecological economics and systems theory have a long-standing history. As a foregrounding metatheoretical framework, systems thinking deepens socio-ecological acuity through comprehensive models of complex relationships between social and biophysical systems. However, critical and soft systems are often overlooked, necessitating a framework for “critical pluralism,” similar to that used by systems theorists themselves. To do this, we argue that ecological economics needs to include paradigm analysis as an integral part of the ecological economic discourse to situate work within sociological paradigms – not just biophysical limits to growth. To help establish a critical pluralism approach, we trained a group of emerging ecological economics scholars to integrate systems thinking more firmly in research approaches. We integrate soft systems methodology and critical systems heuristics to establish foundations for critical soft systems methodology. We then trained emerging scholars on this new methodology. Emergent from the results of this training is a new paradigm of thought, centred on regenerative features, for the future of ecological economics – which is best navigated with critical pluralistic approaches. The results of this training also present lessons for the discipline of ecological economics that help chart out the discipline's tensions.