Spinel iron oxide nanocrystals (NCs) have been reported to have atomic-level core and surface structural features that differ from those of the bulk material. Recent advances in a continuous growth synthesis of metal oxide NCs make it possible to prepare a series of NCs with subnanometer control of size with diameters below 10 nm that are well-suited for investigating size-dependent structure and reactivity. Here, we study the evolution of size-dependent structure in spinel iron oxide and determine how nanoscale structure influences the growth of NCs. We synthesized spinel iron oxide NCs via a continuous growth method that permits layer-by-layer control of size in order to monitor nanoscale structure over 16 core sizes between 3 and 10 nm. X-ray total scattering data were collected and analyzed with pair distribution function (PDF) analysis in order to refine quantitative structural features including cation occupancies that could be used to detect changes both in the oxidation state and the presence of tetrahedrally coordinated cation vacancies in the NCs. We find that the average iron oxidation state increases as core diameters decrease from 8 down to 3 nm. The trend in iron oxidation state can be explained by the oxidation of surface layers in the NCs. For samples exposed to air for several weeks, oxidation appears to cease when a volume equivalent to that of an ∼1.3 nm shell is converted to the more oxidized maghemite. The number of tetrahedrally coordinated cation vacancies also increases as the NC core size decreases. The correlation between the number of these vacancies and the faster growth for smaller NCs suggests that these reactive vacancies may be responsible for the rapid growth observed for nanocrystals with diameters smaller than 8 nm.