In this chapter we will review a few examples of applications of atomic resolution aberration corrected scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy (EELS) to complex oxide materials. These are most challenging systems where subtle changes in structure or chemistry may result in colossal responses in macroscopic physical behavior. Here, we will review how atomic resolution compositional mapping can be achieved in manganite thin films and single crystals, highlighting the importance of considering artifacts during quantification. Besides, minor changes in near edge fine structure may take place when the crystalline environment, and hence nearest neighbor configuration, is modified. These can also be tracked by atomic resolution EELS, as will be shown through the study of binary Fe oxides. Also, examples regarding the study of distributions of point defects such as O vacancies in cobaltite thin films will be discussed. In these materials, a combination of epitaxial strain and defects may promote physical behaviors not present in bulk, such as the stabilization of unexpected spin state superlattices. Last, a study of extended defects such as dislocation lines will be reviewed. In particular, we will show how chemical segregation at dislocation cores in yttria-stabilized zirconia grain boundaries results in the generation of static O vacancies that affect the local electrostatic potential and hence, the macroscopic ionic conduction properties. © 2016.