This article aims to study the intersection between critical realism and complexity theories through the existing literature on complex systems via an engagement with Luhmann’s autopoiesis. With reference to the philosophies of substance and persistence, I build on previous critical realist scholarship and provide an explanation for what the literature has only noted as the limitations and potentials of autopoiesis for complex systems thinking and its compatibility with Critical Realism. By highlighting how Luhmann’s autopoiesis is not a trans-immanent/ perdurantist-exdurantist system, (...) I show first how a trans immanent system through the method of calibration entails a complex causation involving objects in the environment of systems and not just within their boundaries. Second, I explain how a trans-immanent system fits with CR via the Morphogenetic Régulation framework by exploring the theme of crisis in terms of the movement from inadequate to adequate understanding of objects. (shrink)