Recent advances in microfluidics have enabled the controlled production of multiple-emulsion drops with onion-like topology. The multiple-emulsion drops possess an intrinsic core–shell geometry, which makes them useful as templates to create microcapsules with a solid membrane. High flexibility in the selection of materials and hierarchical order, achieved by microfluidic technologies, has provided versatility in the membrane properties and microcapsule functions. The microcapsules are now designed not just for storage and release of encapsulants but for sensing microenvironments, developing structural colors, and many other uses. However, we are still in the infancy stage for the functionalization of microcapsules and their use. The high flexibility of microfluidic technologies will provide unlimited opportunities for a wide range of conventional and unprecedented applications of microcapsules. For example, the microcapsule sensors can be further designed to have a membrane that actively regulates the material transport and a core that emits NIR signals in response to specific biomolecules. Such a microcapsule could be implanted in patients through injection to monitor the in vivo environment without the need for surgery. Furthermore, artificial cells that behave in the same manner to natural cells in many aspects could be implemented. Artificial cells would produce and secrete beneficial chemicals or proteins in the manner by which they are programmed. The only way to design and produce such elaborate micro-compartments is to use microfluidics and its high controllability over size, shape, and composition of multiple emulsions and high reproducibility.