In this manuscript we present a new interpretation of the seismic series that accompanied eruptive activity off the coast of El Hierro, Canary Islands, during 2011–2013. We estimated temporal variations of the Gutenberg‐Richter b value throughout the period of analysis, and performed high‐precision relocations of the preeruptive and syneruptive seismicity using a realistic 3‐D velocity model. Our results suggest that eruptive activity and the accompanying seismicity were caused by repeated injections of magma from the mantle into the lower crust. These magma pulses occurred within a small and well‐defined volume resulting in the emplacement of fresh magma along the crust‐mantle boundary underneath El Hierro. We analyzed the distribution of earthquake hypocenters in time and space in order to assess seismic diffusivity in the lower crust. Our results suggest that very high earthquake rates underneath El Hierro represent the response of a stable lower crust to stress perturbations with pulsatory character, linked to the injection of magma from the mantle. Magma input from depth caused large stress perturbations to propagate into the lower crust generating energetic seismic swarms. The absence of any preferential alignment in the spatial pattern of seismicity reinforces our hypothesis that stress perturbation and related seismicity, had diffusive character. We conclude that the temporal and spatial evolution of seismicity was neither tracking the path of magma migration nor it defines the boundaries of magma storage volumes such as a midcrustal sill. Our conceptual model considers pulsatory magma injection from the upper mantle and its propagation along the Moho. We suggest, within this framework, that the spatial and temporal distributions of earthquake hypocenters reflect hydraulic fracturing processes associated with stress propagation due to magma movement.