The optimization of tungsten trioxide (WO3) nanoparticles produced via hydrothermal synthesis for application in electrochromic (EC) devices is reported. The structure and morphology of the nanoparticles are controlled by changing the acidity of the aqueous solvent added to the sol-gel precursor (peroxopolytungstic acid) during synthesis. Orthorhombic hydrated WO3 nanorods or monoclinic WO3 nanoslabs are obtained when HCl is added, while synthesis only in aqueous medium results in a mixture of both types of polymorphs. Dual-phase thin films are processed by inkjet printing deposition of the nanoparticles in flexible polyethylene terephthalate substrate with indium tin oxide coating (ITO PET) followed by the deposition of the precursor solution. When compared with purely amorphous tungsten oxide films, the dual phase ones present higher optical densities and improved capacity, and cyclability stability. The best results, obtained for orthorhombic hydrated nanoparticles (ortho -WO3 ·0.33H2 O), are due to its high surface area and improved conductivity. Additionally, the ex situ X-ray diffraction (XRD) lithiation studies show evidence of a higher distortion of the monoclinic when compared with the orthorhombic crystallographic structure, which contribute to the inferior EC performance. These results validate the use of inkjet printing deposition with low processing temperatures for EC dual-phase thin films containing optimized nanoparticles which are compatible with low-cost substrates.