Stained-glass windows form an important part of cultural heritage. Short pulse lasers open new opportunities for safe decontamination. In this work, and for the first time, the interaction of sub-nanosecond and femtosecond pulsed lasers with some contemporary stained-glasses has been analyzed exploring their applicability to safely clean stained-glass windows. The results show that, in these materials, damage can be induced using energy levels below damage thresholds due to the heat accumulation in the coating layer that is being eliminated. The latter generates significant thermal stresses on the glass volume, which induce crack formation. In consequence, in order to apply safe stained-glass cleaning protocols, laser parameters have to be selected to control the temperature increase within this layer. To achieve the latter goal, two alternative irradiation procedures were explored in this work. As a first option, a reduction of the effective pulse repetition frequency to values lower than 20 kHz was applied. A second alternative was used for lasers with pulse repetition rates in the hundreds of kHz. In this case, the burst mode was employed controlling the number of pulses emitted and combined with an adequate time lapse selection between two consecutive burst runs. A proof of concept demonstration was carried out on a stained-glass sample from the Cathedral of Cuenca, dated at the end of the XV century.