Magma emplacement in the top unconsolidated sediments of rift basins is poorly constrained in terms of mechanics and associated hydrothermal activity. Our study compares two shallow sills from the Guaymas Basin (Gulf of California) using core data and analyses from IODP Expedition 385, and high-resolution 2D seismic data. We show that magma stalling in the top uncemented sediment layer is controlled by the transition from siliceous claystone to uncemented silica-rich sediment, promoting flat sill formation. Space is created through a combination of viscous indentation, magma-sediment mingling and fluidization processes. In low magma input regions, sills form above the opal-A/CT diagenetic barrier, while high magma input leads to upward stacking of sills, forming funnel-shaped intrusions near the seafloor. Our petrophysical, petrographic, and textural analyses show that magma-sediment mingling creates significant porosity (up to 20%) through thermal cracking of the assimilated sediment. Stable isotope data of carbonate precipitates indicate formation temperatures of 70−90°C, consistent with the current background geothermal gradient at 250−325 m depth. The unconsolidated, water-rich host sediments produce little thermogenic gas through contact metamorphism, but deep diagenetically formed gas bypasses the low-permeability top sediments via hydrothermal fluids flowing through the magma plumbing system. This hydrothermal system provides a steady supply of hydrocarbons at temperatures amendable for microbial life, acting as a major microbial incubator. Similar hydrothermal systems are expected to be abundant in magma-rich young rift basins and play a key role in sustaining subseafloor ecosystems.