Making use of the isospectrality of Supersymmetry transformations, we propose a general and high-fidelity method to prepare gapped topological modes in discrete systems from a single-site excitation. The method consists of adiabatically connecting two superpartner structures, deforming the input state into the desired mode. We demonstrate the method by pumping topological states of the Su-Schrieffer-Heeger model in an optical waveguide array, where the adiabatic deformation is performed along the propagation direction. We obtain fidelities above F = 0.99 for a wide range of coupling strengths when pumping edge and interface states.