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Volcanism is the most widespread expression of cyclic processes of formation and/or destruction that shape the Earth’s surface. Calderas are morphological depressions resulting from the collapse of a magma chamber following large eruptions and are commonly found in subduction-related tectono-magmatic regimes, such as arc and back-arc settings. Some of the most impressive examples of seafloor hydrothermal venting occur within submarine calderas. Here, we show the results of magnetic investigations at two hydrothermally active submarine calderas, i.e., Palinuro Seamount in the Southern Tyrrhenian Sea, Italy, and Brothers volcano of the Kermadec arc, New Zealand. These volcanoes occur in different geodynamic settings but show similarities in the development of their hydrothermal systems, both of which are hosted within calderas. We present a new integrated model based on morphological, geological and magnetic data for the Palinuro caldera, and we compare this with the well-established model of Brothers caldera, highlighting the differences and common features in the geophysical expressions of both hydrothermal systems. For consistency with the results at Brothers volcano, we build a model of demagnetised areas associated with hydrothermal alteration derived from 3D inversion of magnetic data. Both these models for Brothers and Palinuro show that hydrothermal up-flow zones are strongly controlled by caldera structures which provide large-scale permeability pathways, favouring circulation of the hydrothermal fluids at depth.