La2/3Sr4/3MnO3 (LSMO) can exhibit anisotropic electrical transport properties in bulk crystals. Artificial layered heterostructures offer the possibility of confining magnetic moments to two‐dimensional sheets and increasing the anisotropy compared to bulk crystals. As shown by Shah et al. (pp. 1322–1327), an LSMO cation ordered superlattice grown by molecular beam epitaxy exhibited a large enhancement of magnetization in the out‐of‐plane direction upon cooling the sample below 110 K. Atomic resolution structural analysis of the sample reveals the formation of nanopatches of incoherency to the underlying SrTiO3 substrate when cooling the sample below 150 K. This structural transition observed only in superlattices leads to an enhancement of magnetic moment in the out‐of‐plane direction. Atomic resolution electron energy loss spectroscopy shows chemical modulation of oxygen and manganese valence, coordination, and strain in the sample, which confirms the structural nanopatches observed in imaging and electron diffraction.