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We report on the surface chemical and photocatalytic properties of hierarchical ZnO nanorod assemblies synthesized via zinc acetate-based methods and subjected to various pretreatment protocols. The as-prepared ZnO samples were thoroughly washed and thermally treated at different temperatures and durations to remove residual organics from the synthesis. Despite extensive washing, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and X-ray photoelectron spectroscopy revealed significant amounts of residual organic species on the as-prepared ZnO surfaces. Operando DRIFTS demonstrated that annealing to 500 °C was required to effectively eliminate these synthesis-related residues. However, prolonged annealing also led to the removal of two types of ZnO-associated defects: (i) terminal -OH groups, which reformed upon cooling in synthetic air, and (ii) intrinsic lattice defects hosting bridge-bonded OH species, which were irreversibly healed. The catalytic performance of the ZnO samples, assessed by phenol photodegradation and its decomposition products, showed enhanced activity for washed and calcined ZnO (up to 52% degradation) compared to as-prepared samples treated only by chemical washing (24% degradation). Operando DRIFTS revealed that extended thermal treatment at 500 °C led to a decline in catalytic activity (34% degradation) relative to samples exposed to shorter annealing times. This loss in activity was directly correlated with a decreased concentration of catalytically active lattice vacancy defects. Our findings provide molecular-level evidence of two competing effects during thermal pretreatment of ZnO in oxidizing environments: the removal of inhibitory organic residues (which enhances activity) and the healing of reactive lattice defects (which reduces activity). These results underscore the critical importance of optimizing pretreatment conditions when designing efficient ZnO-based catalysts from organic zinc precursors and highlight the essential role of lattice defects in governing ZnO surface reactivity.