Triphenylphosphine ligand-protected Au9 clusters deposited onto titania nanosheets show three different atomic configurations as observed by scanning transmission electron microscopy. The configurations observed are a 3-dimensional structure, corresponding to the previously proposed Au9 core of the clusters, and two pseudo-2-dimensional (pseudo-2D) structures, newly found by this work. With the help of density functional theory (DFT) calculations, the observed pseudo-2D structures are attributed to the low energy, de-ligated structures formed through interaction with the substrate. The combination of scanning transmission electron microscopy with DFT calculations thus allows identifying whether or not the deposited Au9 clusters have been de-ligated in the deposition process.