We investigate the effect of Ni doping on the Fe-site in single crystals of the magnetic superconductor RbEuFe$_4$As$_4$ for doping concentrations of up to 4%. A clear suppression in the superconducting transition temperature is observed in specific heat, resistivity and magnetization measurements. Upon Ni-doping, the resistivity curves shift up in a parallel fashion indicating a strong increase of the residual resistivity due to scattering by charged dopand atoms while the shape of the curve and thus the electronic structure appears largely unchanged. The observed step $Delta C/T_c$ at the superconducting transition decreases strongly for increasing Ni doping in agreement with expectations based on a model of multi-band superconductivity and strong inter-band pairing. The upper critical field slopes are reduced upon Ni doping for in- as well as out-of-plane fields leading to a small reduction in the superconducting anisotropy. The specific heat measurements of the magnetic transition reveal the same BKT behavior close to the transition temperature $T_m$ for all doping levels. The transition temperature is essentially unchanged upon doping. The in to out-of-plane anisotropy of Eu-magnetism observed at small magnetic fields is unaltered as compared to the undoped compound. All of these observations indicate a decoupling of the Eu magnetism from superconductivity and essentially no influence of Ni doping on the Eu magnetism in this compound.