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The influence of stress jump conditions on a steady, fully developed two-layer magnetohydrodynamic electro-osmotic nanofluid in the microchannel, is investigated numerically. A nanofluid is partially filled into the microchannel, while a porous medium, saturated with nanofluid, is immersed into the other half of the microchannel. The Brinkmann-extended Darcy equation is used to effectively explain the nanofluid flow in the porous region. In both regions, electric double layers are examined, whereas at the interface, Ochoa-Tapia and Whitaker's stress jump condition is considered. The non-dimensional velocity, temperature, and volume fraction of the nanoparticle profiles are examined, by varying physical parameters. Additionally, the Darcy number, as well as the coefficient in the stress jump condition, are investigated for their profound effect on skin friction and Nusselt number. It is concluded that, taking into account the change in shear stress at the interface has a significant impact on fluid flow problems. [ABSTRACT FROM AUTHOR]