Black hole (BH) perturbation is followed by a ringdown phase which is dominated by quasinormal modes (QNM). These modes may provide key signature of the gravitational waves. The presence of a deformed spacetime structure may distort this signal. In order to account for such effects, we consider a toy model consisting of a noncommutative charged scalar field propagating in a realistic black hole background. We then analyse the corresponding field dynamics by applying the methods of the Hopf algebra deformation by Drinfeld twist. The latter framework is well suited for incorporating deformed symmetries into a study of this kind. As a result, we obtain the BH QNM spectrum that, besides containing the intrinsic information about a black hole that is being analysed, also carry the information about the underlying structure of spacetime.