Understanding magmatic systems feeding volcanoes is critical for accurate interpretation of monitoring data and, ultimately, eruption forecasting. Following 3 months of precursory unrest, the first historical eruption at El Hierro, Canary Islands, took place ∼2 km offshore from October 2011 to March 2012. Our detailed petrological analysis of lava samples reveals that at least two distinct magmas initially supplied from reservoirs in the mantle underwent hybridization at 15–25 km depth, i.e., also largely within the upper mantle beneath El Hierro. Diffusion chronometry applied to zoned olivine crystals indicates that magma mixing began during the period of preeruptive seismicity and continued for weeks after the eruption onset. Our data also capture a magma stagnation level at 10–15 km depth in the lower crust, consistent with lateral propagation of an intrusion over substantial distances before rapid magma transit to the seafloor. The remarkable spatial and temporal correlation of petrological and geophysical data at El Hierro suggests that the observed seismicity records magma mixing and forceful intrusion as well as subsequent reservoir dynamics. These results demonstrate that eruptions at El Hierro are controlled principally by deep-seated processes, with little influence from shallow crustal levels, and have important implications for monitoring of renewed unrest at long-dormant volcanoes.