In this study, a Schotten-Baumann reaction was optimised in flow using Bayesian optimisation based on qNEHVI acquisition function. The reaction was optimised for two competing objectives space-time-yield and E-factor. The Pareto front and a set of optimal experimental conditions were identified with a small number of experiments (<40 experiments) and significantly shorter calculation time, when compared to a similar, state-ofthe art optimisation methodology. Based on the optimisation results, batch and flow conditions were compared, and the undesired hydrolysis was successfully suppressed by using the flow conditions. The influence of flow rate and solvent choice were further investigated to gain insights into the interactions between reaction and mixing. Partial mixing was found to be unsuitable for this reaction due to hydrolysis, resulting in low yields of the desired product. This work would be useful for developing new chemical processes using organic and aqueous mixed solvent system.