This manuscript investigates the effects of viscous dissipation, Ohmic heating, nonlinear thermal radiation, chemical reactions, Hall current, and ion slip on the mixed convection flow of magnetohydrodynamic (MHD) Casson nanofluid over a vertically stretching sheet in a spongy medium. The strongly nonlinear ordinary differential equations (ODEs) derived from the governing equations are solved using a sixth-order, seven-stage Runge–Kutta (RK6) method in conjunction with the shooting technique. Numerical simulations are conducted using an open-source Python programming language. The study evaluates temperature, velocity, nanoparticle concentration, skin friction coefficients, Nusselt number (rate of heat transfer), and Sherwood number (rate of mass transfer) based on dimensionless parameters. Key findings reveal that increasing ion slip and Hall currents enhance the velocity profile in the x-direction, while the Casson parameter exerts a diminishing effect. The fluid temperature decreases with higher Hall current, Casson parameter, and ion slip values but increases due to nonlinear thermal radiation, the temperature ratio parameter, and the Eckert number. Furthermore, the chemical reaction parameter and Schmidt number reduce nanoparticle concentration within the boundary layer, with the Casson parameter amplifying this effect. The study also examines the rates of mass, heat, and momentum transfer near the surface under varying parameter influences, presenting results through comprehensive graphs and tables. To validate the numerical method, a comparative analysis is conducted against previous studies, demonstrating excellent agreement and thus confirming the reliability and accuracy of the computational approach.