Atomic force microscopy is used to conduct the first detailed nanoscopic study on the crystal growth of a complex mixed metal/metal–organic framework based on the MOF-5 framework topology. Shells of isomorphously substituted Co/Zn-MOF-5 and MOF-5 were epitaxially grown on MOF-5 core crystals at room temperature and low supersaturation to produce complex core–shell–shell structures with a hierarchal mixed metal nature involving mixing at the atomic level in the isomorphously substituted Co/Zn-MOF-5 shell and at the nanometer level through segregation of the Co/Zn-MOF-5 and MOF-5 layers. The presence of cobalt in the growth solutions was found to retard the overall rate of surface growth in comparison to a cobalt-free growth solution and stop growth entirely for a growth solution containing a Zn/Co ratio = 0.6. The presence of cobalt in the growth solutions was also found to affect the relative rates of terrace spreading in different crystallographic directions compared to cobalt-free growth with spreading in the ⟨110⟩ directions decreasing relative to the rate along the ⟨100⟩ directions. The work provides new understanding of the crystal growth of complex mixed metal/metal–organic frameworks and a methodology to prepare these complex forms in a more controlled manner.