In this paper, we present a discretization of the time-dependent Schrödinger equation based on a Magnus-Lanczos time integrator and high-order Gauss-Lobatto finite elements in space. A truncated Galerkin orthogonality is used to obtain duality-based a posteriori error estimates that address the temporal and the spatial error separately. Based on this theory, a space-time adaptive solver for the Schrödinger equation is devised. An efficient matrix-free implementation of the differential operator, suited for spectral elements, is used to enable computations for realistic configurations. We demonstrate the performance of the algorithm for the example of matter-field interaction.