The development of smooth, mirror-like surfaces provides insight into the mechanical behaviour of crustal faults during the seismic cycle. To determine the thermo-chemical mechanisms of fault mirror formation, we investigated carbonate fault systems in seismically active areas of central Greece. Using multi-scale electron microscopy combined with Raman and electron energy loss spectroscopy, we show that fault mirror surfaces do not always develop from nanogranular volumes. The microstructural observations indicate that decarbonation is the transformation process that leads to the formation of smooth surface coatings in the faults studied here. Piercement structures on top of the fault surfaces indicate calcite decarbonation, producing CO2 and lime (CaO). Lime subsequently reacts to portlandite (Ca(OH)2) under hydrous conditions. Nanoscale imaging and electron diffraction reveal a thin coating of a non-crystalline material sporadically mixed with nano-clay, forming a complex-composite material that smooths the slip surface. Spectroscopic analyses reveal that the thin coating is non-crystalline carbon. We suggest that ordering (hybridisation) of amorphous carbon led to the formation of partly-hybridised amorphous carbon but did not reach full graphitisation. Calcite nanograins, <50 nm in diameter, are spatially associated with the carbon and indicate that the decomposition products acted as a crystallisation medium. Within this medium, portlandite back-reacted with CO2 to form nanocrystalline calcite. Consequently, two types of calcite nanograins are present: nanograins formed by grain-size reduction (primary nanograins, >100 nm) and new nanograins formed by back-reaction (secondary nanograins, <50 nm). Hence, we suggest that the new, secondary nanograins are not the result of comminution during slip but originate from pseudomorphic replacement of calcite after portlandite. The continuous coverage of partly-hybridised amorphous carbon on all samples suggests that calcite decarbonation products may develop across the entire fault surface, controlling the formation of carbonate fault mirrors, and may facilitate slip on a decarbonation-product glide film.