Despite rapid recent progress, controlled dopant incorporation and attainment of high mobility in thin films of the prototypical complex oxide semiconductor SrTiO3 remain problematic. Here, analytical scanning transmission electron microscopy is used to study the local atomic and electronic structure of Nb-doped SrTiO3 both in ideally substitutionally doped bulk single crystals and epitaxial thin films. The films are deposited under conditions that would yield highly stoichiometric undoped SrTiO3, but are nevertheless insulating. The Nb incorporation in such films was found to be highly inhomogeneous on nanoscopic length-scales, with large quantities of what we deduce to be interstitial Nb. Electron energy loss spectroscopy reveals changes in the electronic density of states in Nb-doped SrTiO3 films compared to undoped SrTiO3, but without the clear shift in the Fermi edge seen in bulk single crystal Nb-doped SrTiO3. Analysis of atomic-resolution annular dark-field images allows us to conclude that the interstitial Nb is in the Nb(0) state, confirming that it is electrically inactive. We argue that this approach should enable future work establishing the vitally needed relationships between synthesis/processing conditions and electronic properties of Nb-doped SrTiO3 thin films.