A new oscillatory microfluidic junction is described, which enables the consistent formation of highly uniform and complex double emulsions, and is demonstrated for the encapsulation of four different reagents within the inner droplets (called cores) of the double emulsion droplets. Once the double emulsion droplets had attained a spherical form, the cores assumed specific 3D arrangements, the orchestration of which appeared to depend upon the specific emulsion morphology. Such double emulsion droplets were used as templates to produce highly compartmentalised microcapsules and multisomes. Based on these construct models, we numerically demonstrated a model chemical reaction sequence between and within the liquid cores. This work could provide a platform to perform space/time-dependent applications, such as programmed experiments, synthesis, and delivery systems.