The application of atomic layer deposition (ALD) to metal organic frameworks (MOFs) offers a promising new approach to synthesize designer functional materials with atomic precision. While ALD on flat substrates is well established, the complexity of the pore architecture and surface chemistry in MOFs present new challenges. Through in situ synchrotron X-ray powder diffraction, we visualize, how the deposited atoms are localized and redistribute within the MOF during ALD. We demonstrate that the ALD is regioselective, with preferential deposition of oxy-Zn(II) species within the small pores of NU-1000. Complementary density functional calculations indicate that this startling regioselectivity is driven by dispersion interactions associated with the preferential adsorption sites for the organometallic precursors prior to reaction.