Heavy vector mesons produced in a heavy ion collision are important sources of information about the quark gluon plasma (QGP). For instance, the fraction of bottomonium states observed in a such a collision is altered by the dissociation effect caused by the plasma. So, it is very important to understand how the properties of the plasma, like temperature, density and the presence of background magnetic fields, affect the dissociation of bottomonium in the thermal medium. AdS/QCD holographic models provide a tool for investigating the properties of heavy mesons inside a thermal medium. The meson states are represented by quasinormal modes in a black hole geometry. In this work we calculate the quasinormal modes and the associated complex frequencies for the four lowest levels of radial excitation of bottomonium inside a plasma with a magnetic field background. We also calculate the differential configuration entropy (DCE) for all these states and investigate how the dissociation effect produced by the magnetic field is translated into a dependence of the DCE on the field. An interesting result obtained in this study is that the DCE increases with the radial excitation level. Also, a non trivial finding of this work is that the energy density associated with the bottomonium quasinormal modes present a singularity near the black hole horizon. However, as we show here, it is possible to separate the singular factor and define a square integrable quantity that provides the DCE for the bottomonium states.