In the northern Tyrrhenian Sea, late Miocene intrusions (Monte Capanne pluton and Porto Azzurro pluton) were emplaced at upper crustal levels (<0.2 GPa) in the thrust systems of Elba Island. The emplacement of intrusive rocks is currently explained in the context of late Miocene extensional tectonics. New detailed structural data collected along a continuous natural cross section through the contact aureole of the Porto Azzurro pluton (eastern Elba) where strain localization has occurred within two west-dipping decameter-scale carbonate shear zones, namely the Calanchiole and Felciaio shear zones, are reported here. These shear zones, characterized by a lithological difference with calcite and dolomite marbles dominant in the Calanchiole and Felciaio shear zones, respectively, exhibit a similar rheological behavior. They represent two weakened layers in which west-dipping mylonitic foliation, sheath folds, boudinage structures, and upright folds developed within the contact aureole. Moreover, in correspondence with the Felciaio shear zone, the inversion of metamorphic facies occurs. Meso- and microstructural data give evidence that most of the deformation and displacement in the shear zones was coeval with contact metamorphism and developed under metamorphic conditions retrograde from pyroxene hornfels to hornblende-hornfels facies. Geometric and kinematic features indicate that both shear zones correspond to ductile thrusts, which led to internal stacking of the contact aureole. Therefore, at Elba Island, emplacement of intrusive rocks coeval with late Miocene crustal shortening gives a new perspective on relations between tectonics and magmatism in the northern Apennines.