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Abstract Magma emplacement in the top unconsolidated sediments of rift basins is poorly understood. We compare 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, favoring flat sill formation. Space is created through a combination of viscous indentation, magma‐sediment mingling and fluidization processes. We show that sills emplace above the opal‐A/CT diagenetic barrier. Our model suggests that in low magma input regions sills emplace at constant depth from the seafloor, while high magma input leads to upward stacking of sills, culminating in a funnel‐shaped intrusions. 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 suggest carbonate formation at 70–90°C, consistent with 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, serving as an incubator that may be abundant in magma‐rich young rift basins and play a key role in sustaining subseafloor ecosystems.