Despite multidisciplinary evidence for crustal magma accumulation below Santorini volcano, Greece, the structure and melt content of the shallow magmatic system remain poorly constrained. We use three-dimensional (3-D) velocity models from tomographic inversions of active-source seismic P-wave travel times to identify a pronounced low-velocity anomaly (–21%) from 2.8 km to 5 km depth localized below the northern caldera basin. This anomaly is consistent with depth estimates of pre-eruptive storage and a recent inflation episode, supporting the interpretation of a shallow magma body that causes seismic attenuation and ray bending. A suite of synthetic tests shows that the geometry is well recovered while a range of melt contents (4%–13% to fully molten) are allowable. A thin mush region (2%–7% to 3%–10% melt) extends from the main magma body toward the northeast, observed as low velocities confined by tectono-magmatic lineaments. This anomaly terminates northwest of Kolumbo; little to no melt underlies the seamount from 3 to 5 km depth. These structural constraints suggest that crustal extension and edifice loads control the geometry of magma accumulation and emphasize that the shallow crust remains conducive to melt storage shortly after a caldera-forming eruption.