Acrylic polymers were extensively used in past restoration practices, usually as consolidants or protecting agents. Their removal is often required because polymer coatings can improve some decay processes of stone substrates and, after ageing, may generate undesirable materials on the surface of artifacts. Therefore, the removal of old polymer coating from the surface of artifacts has become a common operation in the conservation of cultural heritage. As with other cleaning operations, it is a delicate process that may irreversibly damage the artifacts if not correctly carried out. The main aim of this study was to determine the appropriate cleaning procedure for efficiently removing old acrylic polymers (e.g., Paraloid B-72) from the surface of historical buildings. For this purpose, a polymer was applied to two different porous stone substrates (bio-calcarenite and arenaria stone). The hydrogel cleaning approach was used for the present study, as preliminary results suggested that it is the most promising polymer-removing method. The considered hydrogel (based on a semi-interpenetrating polymer network involving poly(2-hydroxyethyl methacrylate) and polyvinylpyrrolidone) was prepared and characterized using different techniques in order to assess the gel’s properties, including the gel content, equilibrium water content, retention capability, hardness, Young’s modulus, and morphology. After that, the hydrogel was loaded with appropriate amounts of nano-structured emulsions (NSEs) containing a surfactant (EcoSufTM), organic solvents, and H2O, then applied onto the coated surfaces. Moreover, plain EcoSurfTM in a water emulsion (EcoSurf/H2O) was also used to understand the polymer-removing behavior of the surfactant without any organic solvent. A comparative study was carried out on artificially aged and unaged polymer-coated samples to better understand the cleaning effectiveness of the considered emulsions for removing decayed polymer coatings. The experimental results showed that the NSE-loaded hydrogel cleaning method was more effective than other common cleaning procedures (e.g., cellulose pulp method). In fact, only one cleaning step was enough to remove the polymeric material from the stone surfaces without affecting their original properties.