Abstract Stained-glass windows play an important role in cultural heritage. Human and environmental factors have subjected these pieces to risks of damage. Mechanical and chemical-based cleaning methods have been used for their restoration and conservation. Additionally, short-pulse lasers have opened new opportunities for safe and controlled cleaning and restoration of these important materials. In this work, ultra-short pulsed lasers were used to clean an artificially applied coating from the surface of a contemporary colorless glass frequently used in the restoration of stained-glass windows. One of the objectives was to explore the applicability of using these types of lasers to safely clean historical stained-glass windows. It was observed that temperature rise and subsequent heat accumulation in the coating layer being removed was sufficient to generate significant thermal stresses on the underlying glass surface leading to damages even when the laser energies are lower than the damage thresholds. Some laser treatments that limit this heat accumulation were designed in this study. For laser systems operating at frequencies in the range of several hundreds of kHz, the option was to work in burst mode, limiting the number of pulses in each burst and selecting an adequate time lapse between two consecutive burst runs. A method to uniformly clean a given surface is proposed in this work. When lower frequencies are available, treatments using frequencies lower than 20 kHz are enough to safely clean the glass. When UV laser radiation is used, optical damage is also an important aspect to be considered. In this case, the cleaning protocol has to deal with both issues, to avoid heat accumulation and chemical damage.