Abstract: In this paper, we explore the methodological challenge of ensuring coherence between the conceptualisations and assumptions underlying our research and the nature of the methods chosen to tackle our phenomena of interest. We illustrate this challenge by elaborating on the methodological thinking which guided the development of a new method for mapping and analysing changes regarding complex thinking, conceptualised from an enactive, embodied, processual and dynamic perspective. We highlight how our ontological and epistemological assumptions, as well as our pragmatic concerns simultaneously posed challenges and pointed towards solutions, describing broad features of this new visual qualitative method — Complexigraphy — for mapping and analysing changes in complex thinking, while supporting their performance. We propose this method as a potential way of mapping and performing change in complex entities with fuzzy and ill defined boundaries, through a complex process of coupling with the objects, making it particularly suitable for investigating the experience of thinking.