The society has become increasingly interested in using natural products over chemicals for cleaning activities. In this study, the cleaning potential of formulations embedded in a hydrogel matrix and composed respectively of essential oils (EOs) of Origanum vulgare, Thymus vulgaris, and Calamintha nepeta, and their respective main active components (EO-ACs), viz., Carvacrol, Thymol, and Pulegone, on a phototropic biofilm growing on granite was investigated. In addition, and for comparative purposes, analysis with the combination of the three EOs, the combination of the three EO-ACs, and Preventol RI-80® (one of the most effective commercial cleaning agents based on quaternary ammonium salts) in all three cases embedded in a hydrogel matrix, as well as only the hydrogel matrix, distilled water, and Preventol RI-80®, in both latter cases applied with brush, were also studied. The cleaning effect of the treatments was assessed immediately after the treatment and after one and two weeks by color spectrophotometry, a reliable tool to evaluate the presence and vitality of the phototrophs and the cleaning effectiveness in granite. C. nepeta and its active component Pulegone proved to be the most effective and yielded similar results, comparable to those of uncolonized granite, and better than those obtained with Preventol RI-80® applied with brush (most common way), especially at the end of the experiment. These promising first results support the suitable use of the phytochemical compounds used on phototrophs field where there are still few published studies and encourage further investigation toward the evaluation of their exhibited biocidal activity.