The kinetics of the synthesis of tert-butyl peroxy-2-ethylhexanoate were investigated in a capillary microreactor. TBPEH was synthesized from 2-ethylhexanoyl chloride and tert-butyl hydroperoxide in the presence of a strong base, using the Schotten–Baumann method. The peroxyesterification reaction is always in competition with the unwanted acid chloride hydrolysis. The synthesis was carried out with and without a phase-transfer catalyst. The non-catalyzed reaction showed a low rate, which could be incremented by increasing the temperature and the liquid–liquid interfacial area or by using KOH instead of NaOH as base. The peroxyesterification and hydrolysis rates increased with temperature. However, the use of KOH or the increase in interfacial area accelerated only the peroxyester formation, increasing the selectivity towards the desired product. The addition of a PTC enhanced the peroxyesterification rate without changing the hydrolysis rate. Among the screened PTCs, quaternary ammonium salts with longer alkyl chains gave the best performance, up to 25 times faster peroxyesterification. The rate increase was proportional to the PTC amount. The interfacial area had the same effect as in the non-catalyzed reaction. Because of the tremendous increase in the reaction speed due to the PTC, the rate increased with slug velocity. At low slug velocity the reactants in the thin liquid film surrounding the droplets in the capillary are depleted and the peroxyesterification rate decreases. A reaction mechanism is proposed that explains the experimental observation. The corresponding kinetic model predicts the observed reaction rate with 10% accuracy.