Atomic force microscopy has been used to determine the surface crystal growth of two isostructural metal–organic frameworks, [Zn₂(ndc)₂(dabco)] (ndc = 1,4-naphthalenedicarboxylate, dabco = 4-diazabicyclo[2.2.2]octane) (1) and [Cu₂(ndc)₂(dabco)] (2), from a core crystal of 1 for the former and a core–shell 1@2 crystal for the latter. AFM studies show that the surface terrace morphology expressed is a function of supersaturation, with steps parallel to both the <100> and <110> directions being expressed at higher supersaturations for 1, and steps parallel to the <110> direction being expressed solely at low supersaturation for 1 and 2. The crystal growth mechanisms for both 1 and 2 are essentially identical and involve 2D nucleation and spreading of 0.5 nm high metastable sub-layers of the stable extended 1.0 nm high growth terrace. Surface growth features of 2 indicate that there is an in-plane rotational epitaxy between 2 and 1 of 5.9(7)° that may be directed by the synthesis conditions and that intimate mixtures of different domains of ±5.9(7)° rotational epitaxy are not observed to coexist on the several micron scale on the shell surface. The results provide potential routes and understanding to fabricate MOFs of different crystal forms and defect structures, which are necessary for future advanced function of these versatile materials.