Numerous techniques for mammalian cell culture have been developed to mimic the complex in vivo three-dimensional structure of tissues and organs. Among them, the sole use of proteins to create a matrix where cells are embedded already gives rise to self-organized multicellular assemblies. Loading cells in a controlled extracellular matrix along with cell culture and monitoring through a strategy that is compatible with pipetting tools would be beneficial for high throughput screening applications or simply for a standardized method. Here, we design submillimeter compartments having a thin alginate hydrogel shell and a core made of a collagen matrix where cells are embedded. The process, using a microfluidic device, is based on a high speed co-extrusion in air, leading to a compound jet whose fragmentation is controlled. The resulting core–shell liquid drops are then collected in a gelling bath that triggers a fast hardening of the shell and is followed by a slower self-assembly of collagen molecules into fibers. We show how to formulate the core solution in order to maintain cell viability at physiological conditions that otherwise induce tropocollagen molecules to self-assemble, while being able to prevent flow disturbances that are detrimental for this jetting method. Encapsulated Caco-2 cells, mainly used to model the intestinal barrier, proliferate and form a closed polarized epithelial cell monolayer where the apical membrane faces the continuous medium.