This chapter presents an innovative application of the Body Mapping (BM) technique for exploring the embodied experiences of transgender and gender non-conforming (TGNC) individuals. By focusing on the phenomenon of bodily discordance, the misalignment between the subjective “felt body” and the objective “physical body,” the study seeks to assess pre-reflective and implicit dimensions of these experiences. Drawing from phenomenology and art-based research, the chapter outlines a comprehensive four-step protocol combining micro-phenomenological interviews and expressive creative processes. Two case studies of transmasculine participants illustrate how BM facilitates the non-verbal expression of embodied sensations, emotions, and bodily tensions associated with gender dysphoria. The analysis protocol incorporates a multidimensional framework (temporality, spatiality, materiality, and atmosphere), offering novel insights into the bodily and emotional registers of TGNC individuals. This approach highlights the potential of BM not only as a research tool but also as a therapeutic intervention to support the integration of reflective and pre-reflective dimensions of embodied identity. The findings underscore the importance of non-verbal methodologies for addressing complex and often dissociated embodied experiences in TGNC populations.