The present study reports process intensification by ultrasonication of multilayer oil in water (O/W) emulsion stabilized with whey protein isolate (WPI) and sodium alginate (SA). Ultrasonication was employed in both batch and recirculating flow configurations. The effect of process parameters such as pH, SA concentration, and sonication time on droplet size, zeta potential, morphology, physical and oxidative stability of the multilayer emulsion was studied using batch process. It was observed that the emulsion prepared at pH 5, 0.2 wt% SA and 60 s sonication had good bilayer interaction between WPI and SA molecules. Moreover, it was found that sonication if given for a controlled time period can improve the physical and oxidative stability of the emulsion. Further, the ultrasonication based recirculating flow configuration (RFC) was utilized for the preparation of multilayer emulsion at the optimum operational conditions obtained in the batch studies. The emulsions prepared using RFC were found to have better physical and oxidative stability than using batch ultrasonication at the optimum flow rate of 0.5 L/min with 6 recirculation passes. RFC was found to be 2.5 times more energy efficient than batch ultrasonication process for the synthesis of multilayer emulsions.