Advances in microfluidic emulsification have enabled the creation of multiphase emulsion drops, which have emerged as promising templates for producing functional microcapsules. However, most previous micro-encapsulation methods have limitations in terms of capsule stability, functionality, and simplicity of fabrication procedures. Here, we report a simple single-step encapsulation technique that uses an optofluidic platform to efficiently and precisely encapsulate a specific number of emulsion droplets in photocurable shell droplets. In particular, we show, for the first time, that densely confined core droplets within an oily shell droplet rearrange into a unique configuration that minimizes the interfacial energy, as confirmed here from theory. These structures are then consolidated into multi-cored microcapsules with structural and mechanical stability through in situ photopolymerization of the shell in a continuous mode, which are capable of isolating active materials and releasing them in a controlled manner using well-defined nanohole arrays or nanoscopic silver architectures on thin membranes.