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Electrokinetic energy conversion provides a scheme for energy harvesting and storage for on-chip applications. However, the major drawback of electrokinetic energy conversion is its low conversion efficiency. Researchers are in a quest to find ways to improve this efficiency. With the same motive, we investigated the generation of streaming potential by applying surface modification and employing a non-Newtonian fluid to flow through the microchannel under constant pressure difference across its ends. Shear-thickening liquids tend to lessen electrokinetic effects, whereas shear-thinning liquids favour them. Also, having superhydrophobic surfaces improve the magnitude of generated streaming potential. We examine the combined effect of fluid rheology and surface modification on electrokinetic energy generation. We have learned intriguing insights about using non-Newtonian fluid in hydrophobic microchannels as an outcome of our combined research. Hydrophobic surfaces do not enhance the efficiency for a fluid with below a power law index of 0.7. The findings of this research can be used towards the selection of fluid-substrate combination that will optimize electrokinetic power generation efficiency.