Carbon geosequestration (CGS) in geological formations is a technology that can drastically reduce anthropogenic greenhouse gas emissions. The CO2 injected into such storage formations is trapped beneath a cap rock, and it is thus obvious that cap rock sealing efficiency is an essential factor for secure CO2 storage. However, the exact effect of supercritical CO2 exposure to microfractured, clay-rich shale cap rock—note that shale cap rock commonly contains microfractures—is poorly understood. We imaged fractured cap rock shale samples before and after supercritical CO2 injection via x-ray micro computed tomography at high resolution in three dimensions (3.43 μm3) and representative reservoir conditions (i.e., a high pressure of 15 MPa and an elevated temperature of 50°C). Clearly, the fractures closed when flooded with supercritical CO2, which was most likely induced by clay swelling. As a consequence, the fracture permeability dramatically decreased, significantly increasing containment security and derisking CGS projects.