We generalize the potential reconstruction method to set up a dynamical Einstein-Born-Infeld-dilaton model, which we then use to study holographic quarkonium melting in an external magnetic field. The non-linear nature of the model allows to couple the magnetic field to the quarkonium inner structure without having to introduce back-reacting charged flavour degrees of freedom. The magnetic field dependent melting temperature is computed from the spectral functions and suggests a switch from inverse magnetic to magnetic catalysis when the magnetic field increases. We also discuss the differences due to the anisotropy brought in by the external field.