Synmagmatic and solid-state structures within the Naxos pluton and its rim may provide insight into the interplay between plutonism and regional deformation at upper-crustal level. Within the hornblende–biotite granite of western Naxos, synmagmatic foliations display two distinct patterns, onion-skin in the north and tangential to the rim in the south. The two areas are separated by the NE-trending Glinadon fault. Deformed mafic enclaves in the pluton are prolate, with their long axes parallel to the synmagmatic lineation. In contrast, phenocryst distribution analysis, using the Fry method, defines an apparent oblate strain with a horizontal stretching lineation. Planar markers within the pluton progressively steepen through the vertical at the east pluton border. Several lines of evidence, such as dykes intruding axial areas of rim-parallel folds, foliated or folded aplite veins, folds and spaced cleavage in the mollase, and inverted stratigraphy, suggest pluton emplacement and deformation during transpressional deformation. A northward divergent flow regime with magma spreading out mainly from the Naxos fault, and the deflection of both the synmagmatic foliation pattern and the flow lines at the Glinadon fault, suggest that the NE–SW-and N–S-trending faults were active during pluton formation. In the south the pluton has grown by the expansion of dykes occupying P-shear positions with respect with the Naxos fault; in the north a piecemeal block down-drop complements this process and favours voluminous magma concentration. During the late evolutionary stages of pluton construction, the magma chamber was compartmentalized into NE-trending sectors affected by block rotation in an anticlockwise manner. Understanding the role of faults in the emplacement of the Naxos pluton is important for understanding emplacement of other plutons in the Aegean Sea region, since most of them are controlled by N–S- (Ikaria pluton) or NE- (Tinos, Serifos and Delos plutons) trending faults.