We used a range of advanced microscopy techniques to study the microstructure, nanoscale chemistry, and porosity in zirconium alloys at different stages of oxidation. Samples from both autoclave and in-reactor conditions were available, including ZIRLO™, Zr-1.0Nb, and Zr-2.5Nb samples with different heat treatments. Scanning transmission electron microscopy (STEM), transmission Kikuchi diffraction (TKD), and automated crystal orientation mapping with TEM were used to study the grain structure and phase distribution. Significant differences in grain morphology were observed between samples oxidized in the autoclave and in-reactor, with shorter, less well-aligned monoclinic grains and more tetragonal grains in the neutron-irradiated samples. A combination of energy-dispersive X-ray mapping in STEM and atom probe tomography analysis of second-phase particles (SPPs) can reveal the main and minor element distributions respectively. Neutron irradiation seems to have little effect on promoting fast oxidation or dissolution of β-niobium precipitates but encourages the dissolution of iron from Laves-phase precipitates. An electron energy-loss spectroscopy (EELS) analysis of the oxidation state of niobium in β-niobium SPPs in the oxide revealed the fully oxidized Nb5+ state in SPPs deep into the oxide but Nb2+ in crystalline SPPs near the metal-oxide interface. EELS analysis and automated crystal orientation mapping with TEM revealed Widmanstatten-type suboxide layers in some samples with the hexagonal ZrO structure predicted by ab initio modeling. The combined thickness of the ZrO suboxide and oxygen-saturated layers at the metal-oxide interface correlated well to the instantaneous oxidation rate, suggesting that this oxygen-rich zone is part of the protective oxide that is rate limiting in the transport processes involved in oxidation. Porosity in the oxide had a major influence on the overall rate of oxidation, and there was more porosity in the rapidly oxidizing annealed Zr-1.0Nb alloy than in either the recrystallized alloy or the similar alloy exposed to neutron irradiation.