Physical vapor deposition (PVD) is a common method to realize semiconductor thin-films. The optical and electrical properties of e.g. transparent conductive oxide (TCO) layers can be adjusted after deposition by tempering. Flash lamp annealing (FLA) is an ultra-fast post-annealing method using flash lamps to heat the surface of a material. Thus, material characteristics can be altered without thermally loading the substrate below. Because of that, the use of temperature-sensitive substrates is possible. Flash lamp annealing is faster and less cost-intensive than conventional furnace heating. Moreover, it scarcely causes thermo-mechanical stress in the bulk. In this study DC magnetron sputtering with an in-line sheet-to-sheet system was used for thin ITO coatings on glass. The influence of in-line FLA at the in-line machine ILA900 on the thin film properties was investigated systematically. We observed a decrease in sheet resistance and an increase in transmittance in the visible range after FLA. A minimum sheet resistance and a maximum transmittance are reached regardless which pulse duration is used by increasing the energy density. Applying multiple flashes on the same area has no effect on the optical and electrical properties of the thin film but the area of the annealed region increases with an increasing flash number.