We present a theoretical model to determine the effective zeta potential ?eff in microfluidic channels where an embedded, insulated gate electrode allows for external tuning of a portion of the channel surface charge. In addition, we derive a method to determine ?eff in such channels, for any value of salt concentration, using the solution displacement technique. To do so, we simulate typical current-monitoring measurements using our model, and highlight the experimental parameters that lead to inaccurate results using this procedure with an heterogenous channel. Our method corrects for such inaccuracies by using our model with experimental data to find the correct value of ?eff. Finally, we perform experiments to demonstrate our method and the use of our model with a silica-PMDS microchannel system with an embedded Ti-Au-Ti gate electrode that covers 50% of the bottom surface of the channel. We show that our theory captures the salient features of our experiments, thereby offering a useful tool to predict effective zeta potential in channels with a nonuniform zeta potential.