Summary: Solid nano-structures exhibiting fast ion transport (cations moving in anionic crystal structures) are becoming increasingly relevant in industrial applications. However, it is challenging to model their mechanics due to the presence of electromagnetic couplings. In this paper, a mathematical, physical, and computational framework is introduced, for a cation particle moving through an anion sub-lattice structure in the presence of two electromagnetic fields: an external electromagnetic field; and a self-induced electromagnetic field coming from back-reaction phenomena caused by the relative movement of cations with respect to the mentioned structure. Our approach seeks to incorporate magnetic effects, such as magnetic induction and spin of cations, which are not incorporated in other models, mainly due to the intrinsic difficulty of 3D effects. We propose a quantum mechanical formalism based on a Schrödinger-type equation, where a wave function models the behavior of a cation in presence of an external electromagnetic potential, coupled with transient and self-induced electromagnetic effects. To solve the model, a space-time coupled numerical scheme is presented, which allows the possibility of time-evolving electromagnetic effects. The technique uses finite-elements in space and time-marching schemes in time. While a time-explicit marching scheme is used to update the magnetic and electric-potential fields, a time-implicit marching scheme is used to solve the coupled Schrödinger equation. This strategy allows us to update the electromagnetic contributions and wave functions at each time-step. Numerical examples in one and two spatial dimensions (and evolving in time) have been implemented for some meaningful models obtained from nanoionics literature.