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As metal/insulator/metal tunnel junctions (MIMTJs), such as magnetic tunnel junctions and Josephson tunnel junctions, push the insulating tunnel barrier (TB) towards the ultrathin regime (<1 nm) defects inherent in current physical vapor deposition methods become a fundamental obstacle to create pinhole-free and defect-free MIMTJs. Atomic layer deposition (ALD) could offer a solution by providing a conformal, leak-free tunnel barrier with low defect density and atomic thickness as demonstrated recently in ALD Al2O3 tunnel barriers. A question arises on the viability of the ALD TBs in practical circuits of multilayer structures on which increased roughness may occur. To answer this question, this work investigates electron tunneling properties of ALD Al2O3 tunnel barriers of 1.1 –1.2 Å in thickness on half-cell MIMTJs of Al/Fe/Nb fabricated on multilayer structures of different surface roughness using in situ scanning tunneling spectroscopy. Remarkably, the tunnel barriers grown on the raised multilayer device analogue only show a moderate decrease in barrier height from 1.63 eV, to 1.51 eV and to 1.27 eV as the surface roughness increases from 0.9 nm to 2.3 nm, and to 15 nm, alongside a slight decrease in ALD coverage from ∼96%, to ∼93% and 84% on these samples. Overall, these results validate the ALD TBs of atomic thickness for future 3D arrays of devices.