Geological mapping, multiscale structural analysis, and estimations of the degree of fabric evolution and of reaction progress allow the construction of a 3D quantitative model of structural and metamorphic gradients in a portion of continental crust deeply involved in the Alpine subduction system and mainly structured under eclogite-facies conditions before the continental collision. The investigated and modelled rocks outcrop in the surroundings of Mt. Mucrone, in the central Sesia–Lanzo Zone. The Geomodeller® software allowed a quantitative 3D estimation of domains characterized by homogeneous fabric evolution and metamorphic reaction progress (DFE and DRP, respectively) for two of the seven structural and metamorphic imprints detected in this area: the D2-eclogitic and D5-greenschist stages, which are the most pervasive at km scale. Such a 3D modelling clarifies mutual relationships between fabric and metamorphic gradients and indicates that: (i) DFE and DRP are closely related regardless of the rock type; (ii) the syn-deformational thermal regime can influence the degree of metamorphic transformation, if DFE remains below the 60% threshold; (iii) the phase transitions can not be properly implemented in quantitative geodynamic modelling without considering the heterogeneity of reaction progress and fabric evolution.