Laser irradiation enables the removal of unwanted surface deposits from different materials in a safe and controllable manner. Laser parameters should be carefully selected to achieve the removal of the target contaminants without inducing damage to the substrate. Ultra-short pulse lasers have opened new opportunities for safe and controlled decontamination of cultural heritage materials because the thickness of material that is affected by the laser is limited. In this study, an ultraviolet femtosecond pulsed laser was used for the removal of unwanted encrustation formed on the surface of an historical colourless stained-glass sample from the Cuenca Cathedral in Spain. One of the sides of this glass exhibits a reddish-brown grisaille that also has to be preserved. A laser cleaning process has been designed to avoid heat accumulation while controlling the thickness of ablated material. In this context, a multi-step process was selected in order to be able to eliminate, in a controlled way, the crust layer without damaging the grisaille layer, or the glass substrate. In this case, laser irradiation in beam scanning mode with a pulse repetition frequency of 10kHz proved to be effective for the safe cleaning of the glass. The latter was analysed before and after laser cleaning by optical and confocal microscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy, X-ray fluorescence, and Raman spectroscopy, confirming that the crust layer was effectively eliminated without damaging the surface.