External Thermal Insulation Composite Systems (ETICS) are frequently used to enhance the energy efficiency of the built environment. However, stains of presumable biological nature are often detected shortly after application, causing cladding defacement and altering the building aesthetics. To address which microbiota could contribute to these biodeterioration related color/aesthetic anomalies, samples collected from stains detected on the surface of building facades with ETICS in three residential sites in Lisbon, Portugal, were analyzed through microbiological culture-dependent technique and culture-independent amplicon DNA high throughput sequencing taxonomic profiling. The obtained data provided a comprehensive description of microbial communities assigned to diverse taxa of the major microbial groups of heterotrophic bacteria, fungi, cyanobacteria, and microalgae (through DNA plastid detection) in the sampled stains. Based on that, we propose that new microorganisms could be added to the list of bio-susceptibility testing organisms in ETICS. Furthermore, microbiota diversity depended more on facade location and cardinal orientation than on ETICS material composition. Overall, this study reveals the unique microbial communities of color/aesthetic biodeterioration stains in ETICS facades, unlike those of other surfaces, and the associated environmental dynamics.