With a focus on biochemical applications and utilizing relevant physical properties, the current study numerically analyzes the impact of electroosmotic vortex and fluid rheology on the chemical reaction characteristics of species. This is achieved by installing integrated positively charged patches on the extended region of the microreactor with three inlets for injecting the reactants and generating the electroosmotic vortex. In order to produce species “C” in the extended region of the microreactor, it is presumed that reactant species “A” is injected through the upper and lower inlets and reactant species “B” is injected via the intermediate inlet. To solve the associated transport equations with appropriate boundary conditions, a thorough theoretical framework is developed. The results show that the ability of the reactant species to react is boosted when vortices form in the microreactor, increasing the convective mixing strength for reactant species. Furthermore, the fluid rheology significantly affects the reaction characteristics, which is a noteworthy finding. For fluids exhibiting a higher shear-thinning nature, the average concentration of the produced species follows an increasing–decreasing trend with the Carreau number. Additionally, it becomes apparent that the influence of the Damkohler number on the average generated species concentration is negligible at lower Carreau numbers, but it increases with the Damkohler number at higher Carreau numbers. The study also reveals that both rheological and chemical parameters have a substantial impact on the flow rate of product species. Overall, the findings of this investigation provide valuable insights for the development of technologically advanced electroosmotic microreactor capable of effectively generating the intended product species.