The goal of this work is to classify and quantify the factors that govern polyelectrolyte–surfactant complexation in microfluidic confinement and optimize the designs and operating modes of microfluidic reactors to offer additional advantages over the macroscopic synthesis of such complexes. We analyze and solve a system of governing convection–diffusion–reaction equations to conveniently represent these factors or their combinations as dimensionless similarity criteria. We discuss how these factors contribute to the on-chip control of the reaction initiation, the complex product distribution in a microfluidic device, and the phase behavior of the confined reacting flows and experimentally verify the results in microchips. This approach allows for designing microfluidic devices and setting their operating modes to avoid undesirable clogging by reaction products, control the initiation of the complexation reaction, and produce polyelectrolyte–surfactant aggregates with a broader size range and reduced dispersity.