The Philippine Trench marks a nascent plate margin where subduction initiation is propagating from north to south. Magma compositions in the East Philippine Arc record thinning of arc lithosphere as it is eroded from below. Lithosphere is thicker beneath the younger, southern part of the arc, causing basaltic magma to stall and fractionate garnet at high pressure. In the mature, northern section, basaltic magma differentiates at shallower levels, at pressures where garnet is not stable. Local variations in lithosphere thickness suggest that thinning is rapid and may be piecemeal. Fluctuations in arc lithosphere thickness throughout the history of this margin appear to control spatial and temporal variations in magma fluxes into the arc crust. Varying fractionation depths of hydrous basalt may help to explain the andesitic composition of bulk continental crust.