A methodology to engineer roughened inorganic nanostructures on zeolites by deposition and growth of metal hydroxides is reported. Pure-silica (PS) MFI and (aluminosilicate) LTA zeolite crystals are treated by solvothermal methods to deposit inorganic hydroxide (e.g., Mg(OH)2) coatings with nanoscale roughened features on the crystal surfaces in a controlled manner. Detailed characterization of the surface-modified MFI crystals by nitrogen physisorption allows the quantification of the surface roughness of the Mg(OH)2 nanostructures. Pore volume characterization shows that the nanostructure deposition has only a marginal effect on the porosity of the MFI. The surface-roughened zeolites are used to fabricate zeolite/polymer mixed matrix films with considerably improved interfacial adhesion properties. Solvothermal deposition of inorganic nanostructures is also demonstrated on zeolite LTA crystals, which present aluminosilicate surfaces. In this case, the intracrystalline sodium ions in LTA are partially substituted with magnesium ions from the reagent solution during treatment. The solvothermal treatment is thus modified to deposit smaller Mg(OH)2 nanostructures, resulting in more roughened zeolite LTA surfaces. Our detailed characterization reveals that the surface-treated LTA crystals may be promising materials for applications in mixed matrix membranes.