Niobium dioxide can exhibit negative differential resistance (NDR) in metal-insulator-metal (MIM) devices, which has recently attracted significant interest for its potential applications as a highly non-linear selector element in emerging nonvolatile memory (NVM) and as a locally-active element in neuromorphic circuits. In order to further understand the processing of this material system, we studied the effect of thermal annealing on a 15 nm thick NbO2 thin film sandwiched inside a nanoscale MIM device and compared it with 180 nm thick blanket NbOx (x = 2 and 2.5) films deposited on a silicon dioxide surface as references. A systematic transmission electron microscope (TEM) study revealed a similar structural transition from amorphous to a distorted rutile structure in both cases, with a transition temperature of 700 °C for the NbO2 inside the MIM device and a slightly higher transition temperature of 750 °C for the reference NbO2 film. Quantitative composition analysis from electron energy loss spectroscopy (EELS) showed the stoichiometry of the nominal 15 nm NbO2 layer in the as-fabricated MIM device deviated from the target 1:2 ratio because of an interaction with the electrode materials, which was more prominent at elevated annealing temperature.