Quantum materials have emerged as a central focus in condensed matter physics due to their exotic physical properties, many of which are governed by phase transitions that are highly susceptible to external stimuli including temperature, strain, electric fields, and dimensional confinement. This tunability makes these systems not only an ideal platform for probing fundamental physical interactions, but also an eminent class of materials for the development of next-generation electronic and quantum devices. A defining characteristic of many quantum materials is the strong coupling and competition among their electronic, spin, and lattice degrees of freedom. While this competition underpins many of their most desirable properties, it also gives rise to complex inhomogeneities extending to the atomic scale—ranging from phase coexistence and domain structures to active structural defects—that are often also pivotal in determining the material’s macroscopic behavior. Thus, to design and engineer the properties of quantum materials, it is essential to understand these intricate connections between structure and properties across length scales, necessitating characterization techniques with resolution down to the atomic-scale as well as the ability to drive phase transitions, for instance by operating across broad temperature ranges. In this dissertation, advanced cryogenic scanning transmission electron microscopy (STEM) techniques are developed and applied to study two model strongly correlated oxide systems. In the charge-ordered manganite (Bi,Sr,Ca)MnO3, variable-temperature cryogenic STEM imaging reveals how atomic-scale motion of topological defects and reconfiguration of defect networks with temperature underpins changes in macroscopically observable properties through the melting of the charge ordering. In epitaxial thin films of Ruddlesden–Popper Ca2RuO4, the spontaneous formation of elastically stabilized nanoscale stripe patterns—composed of coexisting metallic and insulating phases—is systematically examined across the metal-insulator transition and varying film thicknesses, to explore how strain and dimensionality can be leveraged to engineer novel electronic phase behaviors. Beyond these material-specific insights, this work expands the cryogenic STEM toolkit by enabling imaging and analysis at variable temperatures and over extended length scales. These advances pave the way for broader applications of STEM in studying functional inhomogeneities across a wide spectrum of complex materials.