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Many applications of 2D materials require deposition of non‐2D metals and metal‐oxides onto the 2D materials. Little is however known about the mechanisms of such non‐2D/2D interfacing, particularly at the atomic scale. Here, atomically resolved scanning transmission electron microscopy (STEM) is used to follow the entire physical vapor deposition (PVD) cycle of application‐relevant non‐2D In/In2O3 nanostructures on graphene. First, a "quasi‐in‐situ" approach with indium being in situ evaporated onto graphene in oxygen‐/water‐free ultra‐high‐vacuum (UHV) is employed, followed by STEM imaging without vacuum break and then repeated controlled ambient air exposures and reloading into STEM. This allows stepwise monitoring of the oxidation of specific In particles toward In2O3 on graphene. This is then compared with conventional, scalable ex situ In PVD onto graphene in high vacuum (HV) with significant residual oxygen/water traces. The data shows that the process pathway difference of oxygen/water feeding between UHV/ambient and HV fabrication drastically impacts not only non‐2D In/In2O3 phase evolution but also In2O3/graphene out‐of‐plane texture and in‐plane rotational van‐der‐Waals epitaxy. Since non‐2D/2D heterostructures' properties are intimately linked to their structure and since influences like oxygen/water traces are often hard to control in scalable fabrication, this is a key finding for non‐2D/2D integration process design. [ABSTRACT FROM AUTHOR]