Nanocrystalline tungsten oxide (WO3) films were electrodeposited potentiostatically at room temperature on transparent conducting substrates from an ethanolic solution of acetylated peroxotungstic acid prepared from a wet chemistry process. The changes that occur in the microstructure and the grain size of the as-deposited WO3 films as a function of annealing temperature are simultaneously accompanied by a continually varying electrochromic performance. X-ray diffraction studies revealed the transformation of a nanocrystalline as-deposited WO3 film into a highly crystalline triclinic WO3 as the annealing temperature was raised from room temperature to 500 °C. The microstructural evolution with the increasing annealing temperature of the as-deposited film was further exemplified by transmission electron microscopy (TEM) studies. While the as-deposited film was composed of uniformly distributed ultra fine nanograins, the most noticeable feature seen in these films annealed at 250 °C was the presence of open channels which are believed to promote lithium ion motion. Films annealed at 400 °C exhibited coarse grains with prominent grain boundaries that hinder lithium ion movement, which in turn reduces the film’s ion insertion capacity. In concordance with the TEM results, the 250 °C film had the highest ion storage capacity as it exhibited a charge density of 67.4 mC cm−2 μm−1. The effect of microstructure was also reflected in the high transmission modulation (64%) and coloration efficiency (118 cm2 C−1) of the 250 °C film at 632.8 nm. Contrary to the superior electrochromic performance of the 250 °C film, the optical switching speeds between the colored and bleached states of the as-deposited WO3 film declined considerably as a function of annealing temperature. Also, the diffusion coefficient for lithium ions was greater by at least an order of magnitude for the as-deposited film as compared to the 250 and 500 °C films. In this report, the influence of microstructural changes that are brought about by the annealing of the as-deposited WO3 films on their coloration-bleaching dynamics is evaluated in terms of their structural, electrochromic, and electrochemical properties.