In light of the Joule heating impact, the goal of this work is to examine how electrical conductivity affects the electroosmotic flow characteristics inside wavy microchannels. Leveraging the COMSOL Multiphysics software, thereby a numerical model has been designed to calculate the underlying temperature, potential, and flow fields. Additionally, the experimental findings in the limiting scenario validate the numerical model. Employing a range of physically logical variables for the wavy wall dimensionless amplitude, liquid’s reference electrical conductivity, and reference external electric field, we deeply examined the external electric field, conductive heat lines, flow field, maximum temperature rise, and average flow velocity. Both the electroosmotic flow velocity and the conductive heat flux intensity have been identified to be more intense at bigger amplitudes of the wavy microchannel owing to the enhanced electric field strength located in the throat. An increase in the conductive heat flux intensity, which allows for an increase in the flow velocity magnitude, is brought about by an increase in the liquid’s reference electrical conductivity. As the reference electrical conductivity and electric field intensity increased, it became apparent that the maximum temperature rise also increased. Nevertheless, the same reduces as the wavy wall’s amplitude increases. In response to an intensification in electrical conductivity, the average flow velocity only increases when the reference electric field intensity is high, from 25000 to 50000 V/m. Moreover, as the wave amplitude expands, the flow velocity decreases. Designing an electrical force-driven flow manipulator that produces heat through Joule heating can benefit from the insights drawn from this work.