In the undertaken research, we investigated the preparation route's influence mainly on the surface properties of the final form of Mg-containing zeolite Y. The parent zeolite was subjected to modification with aqueous solutions of magnesium nitrate via impregnation, ion-exchange, and ultrasonic techniques, respectively. The results obtained from the Atomic Force Microscopy (AFM), Computer Tomography (CT), and crystallinity evaluations indicated that the method of zeolite modification influenced the physicochemical properties of the studied samples. Wet impregnation caused additional surface roughness, whereas both ion-exchange and sonication led to surface smoothing of the Mg-containing zeolite Y. Nitrogen adsorption analysis indicated no enormous changes in the porosity of Mg-containing zeolite Y, which can be explained by a relatively high resistance of zeolite to interaction with magnesium nitrate aqueous solutions. However, the biggest changes in porosity were observed for Mg-Y prepared via the impregnation technique due to the longest contact between the zeolite and Mg solution.