The two-dimensional boundary layer flow of a Prandtl nanofluid was explored in the presence of an aligned magnetic field over an inclined stretching/shrinking sheet in a non-Darcy permeable medium. To transform the PDEs of the leading equations into ODEs, a coupled boundary value problem was formed and suitable similarity functions were used. To obtain numerical answers, an efficient code for the Runge–Kutta technique with a shooting tool was constructed with a MATLAB script. This procedure is widely used for the solution of such problems as it is efficient and cost-effective with a fifth-order accuracy. The significance of immersed parameters on the velocity, temperature, concentration, and bioconvection is shown through figures. Furthermore, the physical parameters of the skin friction coefficient and the Nusselt numbers are demonstrated in tables. The declining behavior of the flow velocity against the porosity parameter $K_p$ and the local inertia co-efficient $Fr$ is shown, and the both parameters of the Darcy resistance and Darcy–Forchheimer resistance are responsible for slowing the fluid speed. The increasing values of the Schmidt number $Sc$ decrease the concentration of the nano entities.