WO3/FTO/Glass and WO3:Mo/FTO/Glass thin films were deposited using the pulsed spray pyrolysis technique. The Molybdenum doped thin films were deposited using 2,4,6,8 and 10 % at . concentration in the starting solution. The influence of molybdenum concentration on the structural, electrical, optical and electrochromic properties of WO3:Mo thin films have been systematically studied using Scanning Electron Microscopy (SEM), Selected Area Diffraction Patterns (SAED) in Conventional Transmission Electron Microscopy (CTEM), High Resolution Electron Microscopy (HREM) and Atomic Force Microscopy (AFM). The electrochemical behavior of our materials was studied using cyclic voltammetry both to induce electrochromic behavior and to characterize the electric charge injection and extraction processes. It was found that samples with 2% at. of molybdenum concentration in the starting solution, show the best electrochromic behavior with the highest efficiency and durability. The influence of structural details in our films and their evolution with the molybdenum incorporation, for a fixed substrate temperature on the electrochromic properties of our WO3:Mo thin films has been followed wherever possible.