The efficacy of an electrocoated system that uses a Zr-based conversion coating was assessed to protect galvannealed (GA) steel. The aim was to determine if a Zr-based system has the potential to replace a system with a traditional zinc phosphate (ZnP) conversion coating, where there are concerns for the environmental and economic sustainability. A comparative study between the two conversion coatings, and a control system with no conversion coating, is presented. Data from AC and DC electrochemistry are utilized with surface analysis investigations of pristine specimens, where scanning electron microscopy, x-ray photoelectron spectroscopy, and x-ray diffraction have been used to determine the mechanism through which protection, or coating failure, occurs. Further investigations study surface morphology and stability of specimens during immersion in a simulated electrocoat bath, and their effect on the performance of fully electrocoated systems. The corrosion current density (icorr) for bare, ZnP, and Zr-based conversion coated specimens in chloride-containing solution with no electrocoat were found to be approximately 1.90 µA/cm2, 0.30 µA/cm2, and <0.01 µA/cm2, respectively. Rp values of 0.05 kΩ, 4.2 kΩ, and 20.7 kΩ were recorded for bare, ZnP and Zr-based specimens, respectively. The corrosion current density (icorr) for bare, ZnP, and Zr-based conversion coated specimens under chloride-containing conditions with electrocoat were found to be 3.82 µA/cm2, 0.53 µA/cm2, and 0.06 µA/cm2, respectively. |Z| values at 0.01 Hz (|Z|0.01 Hz) were measured, yielding 45.5 GΩ, 47.4 GΩ, and 31.6 GΩ for bare, ZnP, and Zr-based pretreatments respectively, demonstrating excellent barrier properties after electrocoating. Hydrogen evolution reaction (HER) rate values of 3.52 × 10−2 mol·m−2·s−1, 3.12 × 10−2 mol·m−2·s−1, and 2.94 × 10−2 mol·m−2·s−1 were recorded for the bare, ZnP, and Zr-based systems, respectively. This study produced a ranking order of HER rate. This was bare > ZnP > Zr-based. These results suggest that the Zr-based system is less prone to HER, interfering with the electrocoat deposition process. A performance ranking order for pretreated and electrocoated systems was established, where Zr-based > ZnP > control. The level of thickness and roughness provided by the conversion coating is speculated to be the controlling factor for coating performance, where the ZnP conversion coating was found to provide a thicker layer with greater surface coverage beneficial for a uniform electrocoat film build.