The electrochromism of tungsten oxide occurs through electrochemical reduction, providing active solar control to smart windows, but control over the spectral response is limited and largely empirical. To determine how specific chemical changes result in the optical absorption processes responsible for coloration, we pair structurally well-defined electrochromic nanocrystals (NCs) with cations of varying ionic radii to limit intercalation into specific crystallographic sites. The localized surface plasmon absorption of hexagonal cesium-doped tungsten oxide (Cs:WO3) NCs is enhanced, and new absorption features appear, depending on how the cations intercalate into various interstitial voids. These differences were rationalized using X-ray photoelectron and Raman spectroscopies to reveal the chemical and structural changes leading to the observed variations in the electrochemically induced absorption spectra. Smaller cations, Na+ and Li+, can access additional interstitial sites, leading to a secondary, polaronic mechanism of electrochromism, accounting for enhanced visible light absorption.