Many chemicals used nowadays for the preservation of cultural heritage pose a risk to both human health and the environment. Thus, it is desirable to find new and eco-friendly biocides that can replace the synthetic ones. In this regard, plant essential oils represent effective alternatives to synthetic substances for the preservation of historical monuments. Thymbra capitata (syn. Thymus capitatus) is a medicinal and aromatic plant growing in the Mediterranean area and endowed with important pharmacological properties related to its essential oil. Among them, the antimicrobial ones make the T. capitata essential oil an ideal candidate for industrial applications; for instance, as biocide for the inhibition and elimination of biological patinas of cyanobacteria and green algae on historical monuments. In the present work, we studied the chemical composition of the essential oil from T. capitata growing in Malta by gas chromatography-mass spectrometry (GC/MS). The major volatile component is the phenolic monoterpene carvacrol (73.2%), which is capable of damaging the cytoplasmic membrane and to interfere both in the growth curve and in the invasive capacity, though the contribution of minor components γ-terpinene and p-cymene cannot be disregarded. For the oil application on the stone surface, Pickering emulsions systems were prepared with an essential oil/water 1:3 mass ratio stabilized with kaolinite at 4 mass% in the presence of Laponite®; this allowed to limit the fast volatility of the oil and guaranteed a better application and an easier removal from the artefacts attacked by biodeteriogens both indoor and outdoor. This formulation caused the elimination of biodeteriogens from treated surfaces without residuals or films on artworks surface, and the effect was retained up to four months.