The impact of the environment on stained glass windows produces corrosion processes that have commonly been attributed to chemical agents. However, it has been demonstrated that the combination of relative humidity, dirt and water condensation on the surface of the glass also induces the devlopment of biological species directly involved in corrosion processes. In this work, to distinguish corrosion alterations produced by biotic or abiotic agents, different analyses have been performed. In addition, the effect of dirt, inadequate restorations, and poor maintenance have produced opacity, patina, and black crust in many historical stained glass windows. To eliminate these alterations, various methods using gel systems have been assessed. The results obtained showed the efficacy of different treatments to clean glass surfaces. Various gel-systems were applied on historical glass to reduce the potential risk of toxicity, physico-chemical deterioration of the support, and detachment of polychrome layers from the glass.