This article describes the results of a modeling study performed to understand the microwave heating process in continuous-flow reactors. It demonstrates the influence of liquid velocity profiles on temperature and microwave energy dissipation in a microwave integrated milli reactor-heat exchanger. Horizontal co-current flow of a strong microwave absorbing reaction mixture (ethanol + acetic acid, molar ratio 5:1) and a microwave transparent coolant (toluene) was established in a Teflon supported quartz tube (i.d.: 3·10-3 m, o.d.: 4·10-3 m) and shell (i.d.: 7·10-3 m, o.d.: 9·10-3 m), respectively. Modeling showed that the temperature rise of the highly microwave absorbing reaction mixture was up to 4 times higher in the almost stagnant liquid at the reactor walls than in the bulk liquid. The coolant flow was ineffective in controlling the outlet reaction mixture temperature. However, at high flow rates it limits the overheating of the stagnant liquid film of the reaction mixture at the reactor walls. It was also found that the stagnant layer around a fiber optic temperature probe, when inserted from the direction of the flow, resulted in much higher temperatures than the bulk liquid. This was not the case when the probe was inserted from the opposite direction. The experimental validations of these modeling results proved that the temperature profiles depend more on the reaction mixture velocity profiles than on the microwave energy dissipation/electric field intensity. Thus, in flow synthesis, particularly where a focused microwave field is applied over a small tubular flow reactor, it is very important to understand the large (direct/indirect) influence of reactor internals on the microwave heating process. © 2014 American Institute of Chemical Engineers AIChE J, 2014