Lightweight design in the form of intelligent multi-material structures that combine the advantages of high strength steel and continuous fibre reinforced thermoplastics (CFRTs) gain increasing relevance. In this context, the joining operation is a major challenge as it has to be time and cost efficient and the resulting joint has to exhibit a high mechanical durability. One possible approach is the use of cold formed pin structures, which can be inserted into the CFRT to create a form fitting joint under avoidance of fibre damage as it is commonly the case for bolted or riveted joints. The deformation phenomena of pin joints are usually investigated by macrosectioning or (ex-situ) computed tomography. However, due to resetting elastic deformations and cracks that close after unloading an inaccurate state of the inner joint structure is measured. Furthermore, an investigation of different stages with increasing load and progressing failure is very time consuming, because multiple samples have to be tested and investigated. Alternatively, in-situ computed tomography (in-situ CT) can be used to investigate the testing of pin joints. In this paper, a method for in-situ CT analysis of a single-lap shear test with composite-metal pin joints is presented. The pins are plastically extruded to a height of approx. 1.8 mm from the metal sheet (1.5 mm thick) and are pressed into a locally heated glass fibre reinforced thermoplastic (FRT) sheet (approx. 2 mm thick) creating a form fit. Specimens with quasi-unidirectional fibre reinforcement in 0° and 90° direction are tested. With this procedure, the three-dimensional deformation of the joint can be observed and failure phenomena can be identified for each reinforcement direction respectively. Thus, this method can also be used for validating numerical simulations.