In this study, I integrated geochemical modeling and receiver functions to test for magmatic fractionation above a garnet pyroxenite arc root structure beneath the Colombian magmatic arc (Northern Andes), as a feasible mechanism to explain the record of steep rare earth element (REE) patterns in modern volcanism and the development of an amphibole-rich middle to lower crust. Magmatic fractionation was evaluated through the geochemical modeling of volcanic rocks that show steep REE patterns with high Sr/Y and La/Yb ratios. A well-defined REE geochemical trend was accomplished for all samples at temperature and pressure estimates that are consistent with middle to lower crustal conditions (∼825-935 °C, ∼10.0–14.7 kbar). From the integration of receiver functions, after analyzing the middle to lower crustal signals at multiple stations on top of active volcanoes, the deep crust of the arc is interpreted as a seismically fast (Vs: ≥4.5 km/s) and dense arc root (≥3.3 g/cm3), above which, lies a low-velocity zone with a horizontal to tilted anisotropy axis. This anisotropic low-velocity region is proposed as a partially molten domain related to the evolution of the arc system. The proposed magmatic fractionating model explains satisfactorily the genesis of rocks with steep REE patterns and high Sr/Y (>40) and La/Yb (>20) ratios as a counterpart for a clinopyroxene amphibolite residuum composing deep levels of the arc crust. I suggest that these fractionating processes are playing an important role in the construction of the Colombian magmatic arc, enabling the formation of a dense garnet pyroxenite arc root, a genetically related amphibole-rich middle to lower crust, and the derivation of steep REE patterns with high Sr/Y and La/Yb ratios in the modern Colombian volcanism.