This paper presents a parametric experimental investigation into the electrokinetic instability (EKI) phenomenon within three different types of microfluidic device, namely T-type, cross-shaped, and cross-form with an expansion configuration. The critical electric field strength at which the EKI phenomenon is induced is examined as a function of the conductivity ratio, the microchannel width, the expansion ratio, and the surface treatment of the microchannel walls. it is found that the critical electric field strength associated with the onset of EKI is strongly dependent on the conductivity ratio of the two samples within the microfluidic device and reduces as the channel width increases. The surfaces of the microchannel walls are coated with hydrophilic or hydrophobic organic-based spin-on-glass (SOG) nanofilms for glass-based microchips. The experimental results indicate that no significant difference exists in the critical electric field strengths in the hydrophilic or hydrophobic SOG-coated microchannels, respectively. However, for a given conductivity ratio and microchannel width, the critical strength of the electric field is slightly lower in the SOG-coated microchannels than in the non-coated channels. In general, the results presented in this study demonstrate the potential for designing and controlling on-chip assays requiring the manipulation of samples with high conductivity gradients, and provide a useful general reference for avoiding EKI effects in capillary electrophoresis analysis applications.