Applied systems-thinking involves the use of systems methodologies and concepts to facilitate intervention in social situations. In this area, a body of knowledge has been accumulated to promote informed use of systems methodology. Still, how human experience is considered and used in intervention is limited to what methodologies prescribe or what facilitators do with it. In this paper, we revisit the ideas of autopoiesis and in particular the research project pursued by one of his original authors (Francisco Varela). Following Varela’s intent to develop a middle way in science, we reflect on how applied systems thinking could take a step back regarding how human experience is integrated into intervention. We conclude the paper with a number of suggestions to make applied systems-thinking more permeable and sensitive to human experience and therefore open to compassionate thinking and action.