Committing stone protection to polymeric materials started in the sixties but the study and knowledge of the complex and multiple interactions between stone and polymers has only been carried out recently. It’s important to note that, together with the factors related to the polymeric system itself, intrinsic properties of the stone substrate, like composition, porosity, and crystalline characteristics, play a relevant role. In this paper the issues related to protection of three different Italian marbles have been investigated: Candoglia marble, employed in the building of the Milan Cathedral, Carrara marble, widely used in sculpture and historical architecture, and S. Giuliano marble, used in the building of the Pisa Cathedral and its famous leaning tower. Specimens coming from blocks of the three quarried stones have been characterized, treated with two new partially fluorinated acrylic copolymers, 2,2,2-trifluoroethyl methacrylate/methyl acrylate (TFEMA/MA), and trifluoromethyl-2,2,2-trifluorethyl methacrylate/methyl acrylate (HFIMA/MA), and tested according to UNI-Normal Italian protocol. All the measurements including capillary water absorption, static contact angles, colour variation, water vapour permeability, and SEM morphological analysis have been carried out before and after the polymeric treatment. The aim of this work is to evaluate the protective efficacy of these two new partially fluorinated acrylic copolymers on the three different marbles, and to correlate the different behaviours with the polymers’ properties and with the stone substrates characteristics.