The aim of the study was to incorporate a multidimensional approach to the biodeteriorative influence of aerophytic algal biofilms colonising building materials, such as bricks and plasters in temperature climate zones. Stichococcus sp., Klebsormidium sp., Chlorococcum infusionum, Chlorella vulgaris and Pseudochlorella signiensis were detected in green biofilms covering internal and external walls of buildings in Poland. Their growth led to changes in the material's colour in the range of ΔE = 10.82–37.67, as well high water retention and absorptivity. The moisture content of analysed materials ranged from 9.00 to 14.59%. Further, the direct influence of algal growth on the mechanical properties of the analysed materials was not found. For metabolome analysis laser desorption/ionisation time-of-flight mass spectrometry with silver-109 and gold nanoparticles was used. Derivatives of sulfuric compounds and organic acids were detected but this was not the case for metabolites with well-documented biodeteriorative potential. 109AgNPET LDI MS allowed for the detection of 43 different metabolic pathways, using AuNPET LDI MS 25 pathways. In total, 110 metabolites were found. Although the spectrum of metabolites detected using 109AgNPET LDI MS was broader, AuNPET LDI MS allowed for the detection of pathways that were not found by 109AgNPET LDI MS. The combination of both methods allowed for the widest range of results. •Only green algae grew on facades and more diverse were samples from interior walls.•Algal biofilms caused visible aesthetical biodeterioration ΔE>10.•Higher biomass of algae corresponded to greater moisture of building materials.•Metabolome assays confirmed presence of algal metabolites in samples.•109Ag- and Au NPET LDI MS complement each other giving broadest metabolome profiles.