Atomic layer deposition (ALD) is a gas-phase deposition process based on successive self-terminating gas-solid reactions. During the process, the template substrate is exposed to precursor molecules from the gas phase, which ideally promotes adsorption of a monolayer on the surface. After purging the excess precursor and subsequent exposure to a second gaseous precursor, reaction on the surface of the substrate leads to formation of a layer of the desired material. The layer thickness is controlled by the number of the reaction cycles. Owing to the precise thickness control and broad range of operating temperatures, ALD has recently been used for coating various structures, including thermally and chemically sensitive organic and biological macromolecules. [1][2][3] Much work has also been performed to develop new precursors and new processes to increase the versatility of ALD. For example, a number of studies have been devoted to the investigation of the interface chemistry during the deposition process to achieve better control over the deposition rate and the area selectivity of the deposition. Several reviews about ALD have been recently published. [4][5][6] To date, only little attention has been paid to the chemical interactions between the precursors and the substrate underneath the macroscopic interface formed during the ALD process. It is essential to understand such interactions, particularly as an increasing number of organic soft materials are being used in ALD processes to fulfill various tasks: for example, as masks for area-selective deposition, [1] scaffolds for hybrid material fabrication, [7] or templates for the fabrication of nanostructures.[8] Such materials normally contain various functional groups that are potentially reactive with ALD precursors. Precursors can diffuse through polymer layers during the ALD process, but the chemical interactions between the precursors and the substrate during the diffusion process has only been proposed. [3,9] Herein, we use J-aggregate nanostructures composed of meso-tetra(p-phenylsulfonato)porphyrin (TSPP) or meso-tetraphenylporphyrin (H 2 TPP) as model substrates for standard metal oxide ALD, and show for the first time that the precursor can infiltrate the substrate at the molecular level and induce site-specific metalation. Self-assembly of protonated TSPP molecules into J-aggregate nanotapes occurs through electrostatic interactions between the negatively charged sulfonato groups and positively charged pyrrole amine groups, [10] which are also potential active sites for interactions with ALD precursors. Moreover, the protonated and deprotonated monomer and the J-aggregate of TSPP have distinct light absorption profiles, [11] which provides a convenient method for analysis. Specifically, we show that processing the J-aggregates with standard ZnO-ALD results in infiltration of the metal precursor diethylzinc into the TSPP J-aggregates and induces metalation of TSPP molecules with zinc(II) ions. Formation of the metalloporphyrins was confirmed by UV/Vis...