The eruptive activity of basaltic hotspot volcanoes displays major fluctuations on times scales of years to decades. Theses fluctuations are thought to reflect changes in the rate of mantle melt supply. However, the crustal filter generally masks the mantle processes involved. Here, we show that the cyclic and generally increasing activity of the Piton de la Fournaise volcano (La Réunion) since the mid 20th century is tightly linked to the fertility of its source, as recorded by 87Sr/86Sr and incompatible trace elements ratios of lavas. We identify a twofold control of source fertility on eruptive activity: melt extraction from fertile, incompatible element-enriched veins initiates decadal-scale eruptive sequences, so that vein distribution in the plume source directly controls the cyclic activity. Indirectly, reactive flow of enriched melts increases mantle porosity and promotes melts extraction from the peridotite matrix. This process is thought to have caused a fourfold increase in magma supply between 1998 and 2014 at Piton de la Fournaise, and could also explain magma surges at other frequently active hotspot volcanoes, such as Kilauea, Hawaii. The short-term eruptive activity of hotspot volcanoes appears to be ultimately linked to the distribution and size of lithological heterogeneities in mantle plumes.