AbstractEnhanced coalbed methane recovery and CO2 geostorage in coal seams are severely limited by permeability decrease caused by CO2 injection and associated coal matrix swelling. Typically, it is assumed that matrix swelling leads to coal cleat closure, and as a consequence, permeability is reduced. However, this assumption has not yet been directly observed. Using a novel in situ reservoir condition X‐ray microcomputed tomography flooding apparatus, for the first time we observed such microcleat closure induced by supercritical CO2 flooding in situ. Furthermore, fracturing of the mineral phase (embedded in the coal) was observed; this fracturing was induced by the internal swelling stress. We conclude that coal permeability is drastically reduced by cleat closure, which again is caused by coal matrix swelling, which again is caused by flooding with supercritical CO2.