Megathrust earthquakes rupture hundreds of kilometres of the shallow plate interface in subduction zones, typically at depths of less than 50 km. Intense foreshock activity preceded the 2011 Mw 9 Tohoku-oki (Japan) and 2014 Mw 8.2 Iquique (Chile) megathrust earthquakes. This pre-earthquake activity was thought to be generated1, 2, 3, 4, 5, 6 by slow slip in the seismogenic zone before rupture, but where this slow slip originated and how it spread rapidly over long distances are unknown. Here we analyse seismic activity deep in the subduction zone before the Tohoku-oki and Iquique ruptures, as well as before the 2010 Mw 8.8 Maule earthquake in Chile. We find that, before each of these megathrust earthquakes, shallow seismicity occurred synchronously with bursts of seismic activity deep (~100 km) in the subducting slab. The extensional mechanism of these deep shocks suggests that the slab was stretched at depth. We therefore propose that, before these megathrust quakes, the slab might have started to plunge into the mantle below part of the future rupture zone. We speculate that synchronization between deep and shallow seismicity may have marked the nucleation phase for these three giant earthquakes.