The formation of magmatic plumbing systems in the crust involves mass and heat transfer from deep to shallow levels. This process modifies the local geotherm and increases the thermal maturation of the crust, affecting the rheological state of the host rock and the composition of magma. Here, we report a petrological, geochemical, isotopic and geochronological integrated study of the Huaco (∼354 Ma) and Sanagasta (∼353 Ma, from a new U–Pb zircon age) units from the Carboniferous (Lower Mississippian) Huaco Intrusive Complex, NW Argentina. Similar values of ϵNdt and δ18O, of −3.2 ± 0.7 and +11.2‰ ± 0.3‰ (V-SMOW), respectively, for both units indicate that they shared the same source, as a result of mixing and later homogenization of a crustal component at the Late Devonian (∼378 to 366 Ma), with metasomatized mantle-derived melts. Slightly higher contents of TiO2, FeO, MgO, CaO and rare earth elements for the Sanagasta unit in comparison with the Huaco unit suggest an increase in the degree of partial melting, which may have been caused by a higher temperature at the lower crust. In addition, the previous structural model of the Huaco Intrusive Complex points to an increase in thermal maturation in the upper crust, which drives a change in the emplacement style from tabular subhorizontal (Huaco) to vertically elongated (Sanagasta) bodies. Therefore, the evolution of the intrusive complex may reflect a generalized thermal maturation of the complete magmatic column, at both upper and lower crustal levels.