The potential antifungal activity of the marine alkaloid 2,2-bis(6-bromo-3-indolyl)ethylamine (URB 1204) was firstly assessed by minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) against different fungi. Then, URB 1204 was applied to a building material experimentally contaminated with selected fungi, in single and mixed species, for determining its potential application in preventing fungal growth. In addition, the over-time protection efficacy of URB 1204 was verified, subjecting the treated building surfaces to natural fungal contamination for 6 weeks. URB 1204 showed different antifungal activity, with the lowest MIC value (16 μg/mL) observed against Aspergillus flavus IDRA01, Cladosporium cladosporioides ATCC 16022 and Mucor circinelloides EHS03, and the highest MIC (128 μg/mL) against the dermatophytes strains. The growth Alternaria alternata BC01, Penicillium citrinum LS1, and C. cladosporioides ATCC 16022 on building material treated with URB 1204 water solution (64 μg/mL) was remarkably reduced with an effect time-dependent and related to the examined fungi. In terms of over-time efficacy, the samples treated with URB 1204 showed a delay of fungal growth comparable with that of a commercial antifungal product. These findings evidenced not only the ability of 2,2-bis(6-bromo-3-indolyl)ethylamine to limit the growth of different fungal species on building material but also to provide long-term protection against mold growth and proliferation, opening new perspectives for URB 1204 as preventive agent.