Electromagnetic (EM) radiation has long been recognized as an effective method for enhancing the quality and recovery of heavy and extra-heavy crude oil. The incorporation of EM absorbers, particularly nanoparticles, has demonstrated significant potential to boost efficiency and expand the stimulated reservoir volume. However, the application of simultaneous EM radiation and nanofluid injection in a natural porous medium, which is critical for the successful implementation of this approach in field-scale operations, remains an underexplored frontier. In this context, this research represents a pioneering endeavor, aiming to bridge this knowledge gap through a comprehensive statistical and optimization study. The primary objective was to unravel the intricate interplay between five distinct types of magnetic nanoparticles and their concentrations within the base fluid to improve oil production. Notably, it focused on iron oxide (Fe3O4) magnetic nanoparticles and their innovative hybridization with multi-walled carbon nanotubes (MWCNT) and nickel oxide (NiO) nanomaterial. A newly designed glass sandpack was employed as the porous medium, thus mirroring real reservoir conditions more accurately. Then, a rigorous full factorial design scrutinized the multifaceted effects of nanoparticle type and concentration when introduced into deionized water during this process. The results showed that microwave radiation, applied at 400 W, dramatically improved oil recovery, catapulting it from a baseline of 19% to an impressive 39.5% during water injection. The addition of magnetic nanoparticles to the base fluid enhances efficiency. However, the specific type of nanoparticle exerts varying effects on oil recovery rates. Notably, the synthesis of Fe3O4–MWCNT nanoparticles had a substantial impact on the ultimate oil recovery factor, achieving approximately 69%. Furthermore, the hybridization of Fe3O4 nanoparticles with MWCNT and NiO nanoparticles leads to reduced consumption (using low weight percentages) while achieving the highest oil recovery rates during the injection process. Finally, the optimization analysis demonstrated that employing 0.34 wt.% of Fe3O4–MWCNT nanoparticles under 400 W of microwave radiation represents the optimal condition for achieving the highest oil production in a sandpack porous medium. Under these conditions, the oil recovery factor can increase to 78%.