Based on chemical composition and timing of late Paleogene and Neogene igneous rocks in southern Patagonia, six igneous suites are identified and correlated with subduction processes during the approaching and subduction of active oceanic ridges. Neogene magmatism took place after a period of decreased sub-alkaline magmatism during late Paleogene (LPg Suite). Early Miocene calc-alkaline rocks mark the reactivation of magmatism after subduction acceleration (Suite 1). These rocks are located at ca. 200 km from the trench and are typical products of continental magmatic arcs, where focused metasomatism of the mantle wedge results on high-degree of partial melting (>15%) in a restricted area expressed as a narrow volcanic arc. Contrarily, transitional sub-alkaline to alkaline rocks (Suite 2) were formed during the approaching of the Chile spreading ridge and the subduction of hot oceanic lithosphere (prior to the development of a slab window), where metasomatism encompassed a broader region of the mantle wedge, resulting in lower degrees of partial melting (<15%) and a wider volcanic arc, at ca 200–450 km from the trench. Intermediate igneous rocks with high Sr/Y ratio (Suite 3), located either within a magmatic arc setting, at ca. 270 km from the trench, or in the forearc region (less than 20 km from the trench), were formed during the subduction of the trailing edge of the Nazca plate. Alkaline basalts (Suite 4) are widely distributed, between 220 and 630 km from the trench. They are temporally and spatially related to a slab window generated after the subduction of the Chile Ridge. Andesites with high Sr/Y ratio (Suite 5) from the Quaternary Austral Volcanic Zone, at ca. 160 from the trench, were formed during the subduction of the leading edge of the Antarctica plate. The time and spatial distribution of these suites allow us to propose that the diverse chemical composition of Neogene igneous rocks in southern Patagonia was controlled by varying degrees of metasomatism and partial mantle melting controlled by the thermal structure of the mantle wedge prior, during and after the subduction of an active oceanic spreading ridge. Particularly, the chemical variability and the spatial distribution of Suite 2, which is not common in other magmatic arcs, could be used as a proxy for a warm mantle wedge structure.