We report on atomic-scale transmission electron microscopy (TEM) analysis of Al/AlO_x/Al Josephson junction and the correlation between structure and chemistry of the junction region to its resistance. Al/AlO_x/Al Josephson junctions are fabricated using a variety of process conditions and AlO_x tunnel barriers are compared using STEM imaging and analytical methods. From this study, we observe that the thickness of AlO_x tunnel barriers is not severely impacted by oxidation conditions. To probe the local coordination geometry of Al in the tunnel barrier, we use electron energy loss spectroscopy (EELS). We find that within the AlO_x layers, Al displays both tetrahedral and octahedral coordination. Further, the relative proportion of each coordination depends on the precise process conditions. We discuss the links between these process conditions, oxidation states, and junction resistance in order to identify methods for improving the performance of superconducting qubits.