As an alternative to fossil fuels, biodiesel can be a source of clean and environmentally friendly energy source. However, its commercial application is limited by expensive feedstock and the slow nature of the pretreatment step-acid catalysis. The conventional approach to carry out this reaction uses stirred tank reactors. Recently, the lab-scale experiments using microbubble mediated mass transfer technology have demonstrated its potential use at commercial scale. However, all the studies conducted so far have been at a lab scale~100 mL of feedstock. To analyze the feasibility of microbubble technology, a larger pilot scale study is required. In this context, a kinetic study of microbubble technology at an intermediate scale is conducted (3 L of oil). Owing to the target for industrial application of the process, a commercial feedstock (Spirulina), microalgae oil (MO) and a commercial catalyst para-toluene sulfonic acid (PTSA) are used. Experiments to characterize the kinetics space (response surface, RSM) required for up-scaling are designed to develop a robust model. The model is compared with that developed by the gated recurrent unit (GRU) method. The maximum biodiesel conversion of 99.45 ± 1.3% is achieved by using these conditions: the molar ratio of MO to MeOH of 1:23.73 ratio, time of 60 min, and a catalyst loading of 3.3 wt% MO with an MO volume of 3 L. Furthermore, predicted models of RSM and GRU show proper fits to the experimental result. It was found that GRU produced a more accurate and robust model with correlation coefficient R2 = 0.9999 and root-mean-squared error (RSME) = 0.0515 in comparison with RSM model with R2 = 0.9844 and RMSE = 3.0832, respectively. Although RSM and GRU are fully empirical representations, they can be used for reactor up-scaling horizontally with microbubbles if the liquid layer height is held constant while the microbubble injection replicates along the floor of the reactor vessel—maintaining the tessellation pattern of the smaller vessel. This scaling approach maintains the local mixing profile, which is the major uncontrolled variable in conventional stirred tank reactor up-scaling.