The application of petrography, mineral chemistry, geochemistry, and experimental petrology, including mineral–melt thermodynamic and diffusion modelling, on quenched basanitic magma samples from the recent (2011–2012) submarine eruption of El Hierro (Canary Islands) has permitted the identification of major physico-chemical variations prior to and during magma eruption that correlate in time with monitored geophysical changes. After nearly 3 months of seismic unrest the eruption of El Hierro started on October 10, 2011 and ended by late February 2012. We studied 10 lava balloons and pyroclastic fragments collected floating on the sea surface between October 15 and late January. Based on petrological and geophysical data we distinguish two main eruptive episodes. Magma erupted from the beginning of the eruption until late November 2011 was an evolved basanite (≈5 wt % MgO), changing to more primitive compositions (≈8–9 wt % MgO) with time, thus suggesting extraction from a compositionally zoned magma system. Experimental data and mineral–melt thermodynamic modelling indicate that the erupted magma equilibrated at a pressure of about 400 MPa, which corresponds to a depth of 12–15 km. This depth is consistent with the location of the crust–mantle discontinuity beneath El Hierro and with the hypocentral location of seismicity during the unrest episode. Preliminary modelling of the olivine chemical zoning of crystals erupted in this first episode suggests that the time scale for basanite fractionation and magma replenishment in the shallower reservoir was of the order of a few months. This is within the same time frame as the duration of the unrest episode preceding the eruption. The first eruption episode coincided with intense seismicity mostly located north of the island, first at a depth of 20–25 km and a few days later also at 10–15 km depth, with strong seismic tremor beneath the vent site. An abrupt change in magma composition and crystal content was observed at the end of November 2011. After that, more primitive and less viscous magma erupted contemporaneously with a change in the frequency and intensity of seismic events. During this period, seismicity was mostly north of the island at depths of 10–15 km. At the same time the tremor intensity at the eruption site significantly dropped. This marked the onset of the second eruption episode, which is correlated with an intrusion of fresh, more primitive magma into the shallow magmatic system that raised the temperature of the remaining magma. Experiments reveal that subtle changes in temperature of about 50°C (i.e. 1100–1150°C) were enough to produce large changes in the crystal content (10–60 wt %). This non-linear behaviour between crystal content and temperature had important effects on magma dynamics during transport and cooling. Our results suggest the existence of two interconnected mafic magma reservoirs during the El Hierro eruption, which agrees with the pattern shown by the seismicity. Stress readjustments of the plumbing system, caused by decompression during the eruption, influenced the thermodynamic evolution of the erupting magma and facilitated the intrusion of the deeper magma into the shallow reservoir, thus forcing a change in its rheological characteristics and eruption dynamics.