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Santorini volcano has a history of caldera‐forming eruptions, most recently in the Late Bronze Age, at 3.4 kya, and remains volcanically active. The Kolumbo submarine volcano, located 7 km to the northeast of Santorini, erupted in 1650 AD in a deadly phreatomagmatic eruption. Ongoing seismic activity and active hydrothermal venting at Kolumbo indicate this volcano is a significant hazard to the Santorini region. The magma source for Santorini and the Kolumbo edifice are considered separate in the shallow crust, though their deeper magma distribution is not yet constrained. In this study, we improve constraints on the mid‐crustal magma system of Santorini caldera and the nearby Kolumbo volcano using local earthquake tomography. We use 1515 P‐wave and 1435 S‐wave arrival times from 63 local earthquakes with magnitudes from 0.5 to 3.0 that occurred between 5 and 15 km depth together with an existing data set of active source Pg arrivals. The upper crustal magma system beneath Santorini is imaged to at least 6 km depth, and to 12 km depth beneath Kolumbo. We recover a high P‐wave velocity layer (∼6–8 km) under the Kolumbo magma reservoir that we infer is a rheologically strong seismogenic layer. We also recover a mid‐crustal magma body below 8 km depth located to the NE of Santorini and Kolumbo.