We present kinetic partitioning data for trace cations measured in zoned clinopyroxene crystals obtained from a variably cooled and decompressed olivine basalt erupted at Mt. Etna volcano in Italy. Supersaturation effects and compositional heterogeneities at the interface melt lead to the development of sector zoning, concentric zoning, and patchy zoning in clinopyroxene crystals. Apparent partition coefficients between compositionally different growth layers and adjacent melts (Di) for isovalent groups of trace elements are tested for internal consistency on the thermodynamic basis of lattice strain (ΔGstrain) and electrostatic (ΔGelec) energies of substitutions. The excess energy of partitioning (ΔGpartitioning) for trace cations in zoned crystals accounts for a kinetic incorporation control leading to large enthalpic effects through distortion of the lattice and changes in the electrostatic forces. ΔGpartitioning depends upon the complementary relationship between ΔGstrain and ΔGelec, which is the most appropriate thermodynamic description for the accommodation of rare earth elements and high field strength elements in the lattice site of zoned crystals. Polyhedral sectors, skeletal forms, and overgrowth zones have Di values settled by the number of charge-balanced and -imbalanced configurations taking place in the lattice site as a function of aluminium in tetrahedral coordination, and crystal structural changes produced by heterovalent cation substitutions. In an energetically unstable macroscopic system ruled by cooling and decompression, thermodynamic requirements for the crystallochemical control of Di encompass the attainment of local equilibrium at the crystal-melt interface via the establishment of small-volume reaction kinetics. The requisite of local interface equilibrium is however susceptible to the anisotropic growth velocity of each specific clinopyroxene surface, thereby giving reason to different energetic properties of the crystallographic site. This axiomatic control requires that transition metal cations partition also in consideration of electronic effects related to the crystal field stabilization energy. The overriding implication is that Di values for trace cations having different size, charge, and electronic configuration serve as sensitive probes of the different crystal growth mechanisms, surface incorporation sites, and arrangements of atoms at the lattice-scale. In this perspective, fractional crystallization modeling of 2011–2013 bulk rock data from lava fountains indicates that the compositional evolution of magmas erupted at Mt. Etna cannot be described by a unique equilibrium value of Di for a given clinopyroxene-melt interface. The leverage of interface kinetics is distinctively dominant along the subvolcanic plumbing system, thereby requiring that values of Di differ for structurally and compositionally distinct zones in clinopyroxene phenocrysts. To successfully interpret the trace element signature of Etnean magmas, the archetypal constancy of partition coefficient at bulk thermodynamic equilibrium must be in some measure reappraised in favor of the establishment of a local interface equilibrium upon highly dynamic crystallization and growth conditions.