Our ability to directly characterize the atomic and electronic structures is crucial to developing a fundamental understanding of structure-property relationships in complex-oxide materials. Here, we examine one specific example, the misfit-layered thermoelectric material Ca 3Co 4O 9, which exhibits a high Seebeck coefficient governed by spin-entropy transport as well as hopping-mediated electron transport. However, the role of oxygen and its bonding with cobalt in thermoelectric transport remains unclear. We use atomic-resolution annular bright-field imaging to directly image the oxygen sublattice and to combine our experimental data with multislice image calculations to find that the oxygen atoms in the CoO 2 subsystem are highly ordered, while the oxygen-atomic columns are displaced in the Ca 2CoO 3 subsystem. Atomic-column-resolved electron energy-loss spectroscopy and spectrum image calculations are used to quantify the bonding in the different subsystems of incommensurate Ca 3Co 4O 9. We find that the holes in the CoO 2 subsystem are delocalized, which could be responsible for the p-type conductivity found in the CoO 2 subsystem.