Thin film synthesis methods developed over the past decades have unlocked emergent interface properties ranging from conductivity to ferroelectricity. However, our attempts to exercise precise control over interfaces are constrained by a limited understanding of growth pathways and kinetics. Here we demonstrate that shuttered molecular beam epitaxy induces rearrangements of atomic planes at a polar / non-polar junction of LaFeO$_3$ (LFO) / $n$-SrTiO$_3$ (STO) depending on the substrate termination. Surface characterization confirms that substrates with two different (TiO$_2$ and SrO) terminations were prepared prior to LFO deposition; however, local electron energy loss spectroscopy measurements of the final heterojunctions show a predominantly LaO / TiO$_2$ interfacial junction in both cases. Ab initio simulations suggest that the interfaces can be stabilized by trapping extra oxygen (in LaO / TiO$_2$) and forming oxygen vacancies (in FeO$_2$ / SrO), which points to different growth kinetics in each case and may explain the apparent disappearance of the FeO$_2$ / SrO interface. We conclude that judicious control of deposition timescales can be used to modify growth pathways, opening new avenues to control the structure and properties of interfacial systems.
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