As lightweight design gains more and more attention, time and cost-efficient joining methods such as clinching are becoming more popular. A clinch point’s quality is usually determined by ex situ destructive analyses such as microsectioning. However, these methods do not yield the detection of phenomena occurring during loading such as elastic deformations and cracks that close after unloading. Alternatively, in situ computed tomography (in situ CT) can be used to investigate the loading process of clinch points. In this paper, a method for in situ CT analysis of a single-lap shear test with clinched metal sheets is presented at the example of a clinched joint with two 2 mm thick aluminum sheets. Furthermore, the potential of this method to validate numerical simulations is shown. Since the sheets’ surfaces are locally in contact with each other, the interface between both aluminum sheets and therefore the exact contour of the joining partners is difficult to identify in CT analyses. To compensate for this, the application of copper varnish between the sheets is investigated. The best in situ CT results are achieved with both sheets treated. It showed that with this treatment, in situ CT is suitable to properly observe the three-dimensional deformation behavior and to identify the failure modes.