The secondary metabolite production of several fungal strains of Aspergillus creber, Aspergillus jensenii, Aspergillus penicillioides, Aspergillus protuberus, Aspergillus vitricola, Cladosporium cladosporioides, Eurotium chevalieri, Eurotium halophilicum, Penicillium brevicompactum and Penicillium chrysogenum were characterised by liquid chromatography tamdem mass spectometry. All fungi were isolated from both air and book covers as well as from settled dust from a contaminated library in Venice (Italy). For A. creber and A. jensenii, we identified sterigmatocystin, methoxysterigmatocystin, versicolorin A and related precursors/side metabolites from the biosynthetic pathways. Deoxybrevianamid E, neoechinulin A, pseurotin A and D, and rugulusovin were principally detected from the strains of E. halophilicum, an emerging fungal species implicated in book contaminations in specific indoor niches. The analysis of settled dust showed a wide range of toxic or bioactive fungal metabolites. Forty-five different metabolites were identified in different concentrations; in particular, high amounts of asperglaucide, alamethicin, andrastin A, terrecyclic acid and neoechinulin A were detected. Also one bacterial metabolite, chloramphenicole was detected. This study increases the knowledge about metabolite production of several fungal species, as well as on the indoor presence of fungi that are not detected by aerobiological sampling. These results emphasise how routine dusting operations are necessary and essential in order to prevent further microbiological developments in library environments.