Advances in synthesis and characterization capabilities enable the atomic-scale features and properties of engineering materials to be measured, understood, and controlled in ways that have not previously been possible. Technologically important examples include heterogeneous catalysts, such as nanoporous aluminosilicate zeolites and mesoporous nitrogen-containing carbons, whose hydrocarbon conversion and electrocatalyst properties have been challenging to understand and control. This has been due in part to their non-stoichiometric compositions, semi-crystallinity, and heterogeneous surfaces, which result in complicated structural order and disorder that have important influences on their adsorption and reaction behaviors. By using a combination of X-ray diffraction, electron microscopy, solid-state NMR spectroscopy, molecular modeling, and bulk property analyses, such materials can be probed over multiple length scales to obtain and correlate insights on local bonding environments and interactions with macroscopic catalytic properties. Recent results will be presented on understanding catalyst compositions and structures at an atomic level, in particular the influences that heteroatom distributions, supported metal species, and diverse surface sites have on catalyst reactivities. The analyses provide guidance for the rational design and engineering of catalysts for hydrocarbon conversion, pollution mitigation, and electrochemical device applications.