Detailed microstructural investigations of naturally deformed carbonate rocks are of interest for unraveling potential co-seismic deformation mechanisms. The spatial separation of macroscopic rheological behaviours has led to independent conceptual treatments of frictional failure, often referred to as brittle, and viscous deformation. Here, we investigate the deformation mechanisms that were active in two carbonate fault zones in Greece by performing detailed slip-system analyses on data from automated crystal-orientation mapping transmission electron microscopy and electron backscatter diffraction. We combine the slip system analyses with interpretations of nanostructures and predictions from deformation mechanism maps for calcite. The nanometric grains at the principal slip surface should deform by diffusion creep but the activation of the (0001) slip system is evidence for a contribution of crystal plasticity. A similar crystallographic preferred orientation appears in the cataclastic region of the fault rock despite exhibiting a larger grain size and a different fractal dimension compared to the principal slip surface. The cataclastic region exhibits microstructures consistent with activation of the (0001) and {10-14} slip systems. Post-deformational, static recrystallisation and annealing produces an equilibrium microstructure with triple junctions and equant grain size. We propose a cyclic repetition of plastic strain and annealing, which reduces the grain size and offers an alternative mechanism to form a cohesive nanogranular material. This mechanism leads to a grain-boundary strengthening effect resulting in slip delocalisation which is observed over six orders of magnitude (μm–m) and is expressed by multiple faults planes, suggesting cyclic repetition of deformation and annealing over the seismic cycle.