This theoretical study thoroughly examines the complexities of fluid flow and heat transfer within microfluidic devices by employing anisotropic porous media with wavy walls. The effect of anisotropic permeability and electromagnetohydrodynamics (EMHD) on nanofluid transport is examined in a wavy microchannel under a constant pressure gradient. The nonlinear coupled governing equations for electric double-layer potential, velocity, temperature, and nanoparticle volume fraction are solved numerically using shooting techniques with the Runge–Kutta method. The numerical results are validated with the asymptotic analytical solutions. We explore the impact of parameters like the Hartmann number, Darcy number, and joule heating on nanofluidic flow. The interplay between anisotropic permeability ratio and angle significantly influences flow, temperature profiles, and nanoparticle volume fraction. Reduction in nanoparticle concentration is attributed to constrained entry into the porous medium due to elevated anisotropic permeability. Frictional heating, influenced by the Forchheimer inertial effect, enhances temperature and induces slug flow at low Darcy numbers. The Nusselt number peaks at low Darcy numbers with an anisotropic angle of φ=π/2, experiencing a minimum when φ=0. These findings deepen our understanding of the role of anisotropic permeability in shaping fluid flow and heat transfer in microfluidic systems influenced by EMHD effects.