Although spray drying is a scalable route for particle formation with easy product recovery, a typical spray drier produces broad distributions of particles with various morphologies in a single batch, due to the non-uniform formation of droplets, wide spray trajectories, and various residence times experienced by the droplets during drying. Thus any attempt to interpret the resulting particle functionality directly in relation to their physico-chemical properties is difficult. Here, uniform silica-based microencapsulates encapsulating vitamin B₁₂ homogenously distributed within their matrix were synthesised in a single step via a micro-fluidic-jet-spray-dryer (MFJSD), utilising a micro-fluidic-aerosol-nozzle (MFAN) for continuous generation of monodisperse droplets. We investigated the effects of lactose and Na-alginate to the properties of the silica matrix, as well as the overall particle shapes. The uniform nature of the particles allowed direct correlations between the matrix properties and the release behaviour of vitamin B₁₂ to be observed without the complications of wide size distribution or variety of shapes. Spherical particles with relatively smooth surface were obtained with lactose addition, while incorporation of Na-alginate resulted in increasing surface roughness. Lactose accelerated the release of the encapsulated vitamin B₁₂ (VB12), due to the relatively fast lactose dissolution that allowed buffer to penetrate deep into the matrix to facilitate diffusion and silica erosion. On the contrary, Na-alginate slowed down the release considerably by serving as an additional barrier to decelerate the matrix erosion, as well as due to ionic attraction to the VB12 molecules. Release kinetics data indicated diffusion as the main release mechanism independent of the microencapsulate composition. The release profiles from different compositions of the synthesized particles demonstrated good agreements with the computational predictions, highlighting the ability to modulate the release behaviour directly from the precursor compositions.