This work links mineral-scale deformation mechanisms with structural evolution during subduction, providing examples showing how grain-scale heterogeneities facilitated viscous creep in calcite at nominally seismogenic temperatures. Carbonates commonly enter subduction zones, either highly concentrated in irregularly distributed sediments or as more distributed precipitates in seafloor volcanics. We present shear zones, localized in calcite veins formed during shallow subduction of calcareous sediment and seafloor volcanics, with viscous shear strains of ≥5. Shear strain localized because secondary phases and chemical variations maintained fine grain sizes in calcite aggregates, activating relatively rapid grain size-sensitive and frictional-viscous creep at temperatures (260±10°C), cooler than predicted from extrapolation of experimental data. Creep at increased strain rates may limit elastic strain accumulation during interseismic periods, reducing the likelihood of large megathrust earthquakes. As shown here for calcite, common inherited natural heterogeneities may induce weakening of viscous mechanisms in other rocks, or at larger scales in the lithosphere.