Natural derivatives, such as essential oils, are presented as an alternative to classical biocides to the treatment of biocolonization. Thus, in this work, the cleaning and biocidal potential of some natural derivatives towards two natural biofilms’ growth on the same granite wall, with different microbial composition, was evaluated. For this purpose, three essential oils (EOs) (from Origanum vulgare, Thymus vulgaris and Calamintha nepeta) and their main active principles (APs) (carvacrol, thymol and R-(+)-pulegone, respectively) were embedded in a hydrogel matrix, with different combinations of EOs and APs, in order to evaluate the synergistic action of different actives. For comparative purposes, pure hydrogel and a mechanical method (brushing) were also used. Colorimetric measurements and chlorophyll a fluorescence analyses were performed to evaluate the cleaning action of the treatments on the biofilms. Overall, the EOs and APs present in the hydrogel proved to be reliable treatments to limit natural biocolonization, with O. vulgare being one of the most effective treatments in combination with other compounds, due to the majority presence of carvacrol. Moreover, the effect of the different treatments strictly depended on the biofilm in question, as well as its ability to adhere to the substrate.