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Compartmentalised structures based on lipid-stabilised double emulsions (multisomes) have recently attracted great interest in translational healthcare as potential micro-bioreactors for the synthesis of high-end materials, in situ drug synthesis and delivery, encapsulation of small molecules and cells, and as building blocks for cell-like structures in bottom-up synthetic biology. In contrast to surfactant-stabilised systems, lipid-stabilised systems are particularly more challenging to fabricate, mainly because many materials and surface modification techniques are incompatible with lipids. This paper demonstrates a robust and versatile microfluidic technology for the automated generation of miniaturised multisomes of pL volume in high-throughput using biologically relevant phospholipids.