Algal biofilms contribute to the biodeterioration of building materials (BMs), while restrictions on conventional algicides stimulate the search for sustainable protection strategies. This study evaluated the antialgal potential of selected essential oils and active compounds, with particular emphasis on lemongrass essential oil (LGC), for the control of microalgal biofilms on brick and render surfaces. Three essential oils (Lavandula angustifolia, Melaleuca alternifolia, and Cymbopogon citratus) and two active compounds, eugenol (EU) and geraniol, were screened against terrestrial microalgal strains associated with biodeterioration. Antialgal activity was assessed based on minimum inhibitory and algicidal concentrations. LGC and EU inhibited microalgal growth, reducing photosynthetic activity, chlorophyll a content, and inducing cellular alterations. Metabolomic analysis revealed a strong stress response involving membrane lipid remodeling, oxidative stress, and disruption of photosynthetic metabolism. LGC and EU caused cellular damage, with LGC inducing faster degradation and EU enabling partial adaptation. LGC effectively reduced microalgal biofilms on brick and render, decreased photosynthetic activity, and partially restored surface coloration, without causing significant changes in substrate pH or water absorptivity. Effectiveness depended on biofilm maturity and substrate characteristics. The integrated microbiological, physiological, metabolomic, and material-based approach confirmed the potential of LGC as a sustainable component of future protective coatings for mineral BMs.