The polycondensation reaction to produce polydextrose can be intensified by using micro-process engineering. Fluid Guiding Elements are additively manufactured internal inserts that have already shown their potential to intensify heat transfer in double-pipe heat exchangers. This study investigated the intensification of the polydextrose yield when these internal inserts were used. Different reactor lengths and internal inserts geometries, as well as different operating conditions, were analyzed. The experiments showed that the reactant concentration had no effect on the product yield. Furthermore, it was shown that the process could be intensified at higher temperatures, with relatively low residence times and lower pressures. It was confirmed that the good heat transfer characteristics of the internal inserts allow them to continuously evaporate water during the reaction and to further reach the required reaction temperature, thus shifting the equilibrium towards the desired product. These findings are of special significance for the optimization of the polycondensation reaction of polydextrose.