Recent developments in automotive and aircraft industry towards a multi-material design pose challenges for modern joining technologies due to different mechanical properties and material compositions of various materials such as composites and metals. Therefore, mechanical joining technologies like clinching are in the focus of current research activities. For multi-material joints of metals and thermoplastic composites thermally assisted clinching processes with advanced tool concepts are well developed. The material-specific properties of fibre-reinforced thermoplastics have a significant influence on the joining process and the resulting material structure in the joining zone. For this reason, it is important to investigate these influences in detail and to understand the phenomena occurring during the joining process. Additionally, this provides the basis for a validation of a numerical simulation of such joining processes. In this paper, the material structure in a joint resulting from a thermally assisted clinching process is investigated. The joining partners are an aluminium sheet and a thermoplastic composite (organo sheet). Using computed tomography enables a three-dimensional investigation that allows a detailed analysis of the phenomena in different joining stages and in the material structure of the finished joint. Consequently, this study provides a more detailed understanding of the material behavior of thermoplastic composites during thermally assisted clinching.