The assembly of nanomaterials into suprastructures offers the possibility to fabricate larger scale functional materials, whose inner structure strongly influences their functionality for a vast range of applications. In spite of the many current strategies, achieving multi-compartment structures in a targeted and versatile way remains highly challenging. Here, we describe a controllable and straightforward route to create uniform suprastructured materials with a multi-compartmentalized architecture by confining primary nanocapsules into droplets using a cross-junction microfluidic device. Following solvent evaporation from the droplets, the nanocapsules spontaneously assemble into precisely sized multi-compartment particles, which we term supracapsules. Thanks to the process, each spatially separated nanocapsule unit retains its cargo and functionalities within the resulting supracapsules. However, new collective properties emerge, and, particularly, programmable release profiles that are distinct from those of single-compartment capsules. Finally, the suprastructures can be disassembled into single-compartment units by applying ultra-sonication, switching their release to a burst-release mode. These findings open up exciting opportunities to fabricate multi-compartment suprastructures incorporating diverse functionalities for materials with emerging properties.