Health issues of residents of mold-infested housing are reported on a regular basis, and reasons for the arising impairments can be manifold. One possible cause are the toxic secondary metabolite produced by indoor microfungi (mycotoxins). To enable a more thorough characterization of the exposure to mycotoxins in indoor environments, data on occurrence and quantities of mycotoxins is essential. In the presented study, 51 naturally mold-infested building material samples were analyzed applying a previously developed method based on ultra-high performance liquid chromatography (UHPLC) separation in combination with triple-quadrupole mass spectrometry (TQMS) detection. A total of 38 secondary metabolites derived from different indoor mold genera like Aspergillus, Fusarium, Penicillium, and Stachybotrys were analyzed, of which 16 were detectable in 28 samples. As both the spectrum of target analytes and the investigated sample matrices showed high chemical varieties, an alternative calibration approach was applied complementary to identify potentially emerging matrix effects during ionization and mass spectrometric detection. Overall, strong alterations of analyte signals were rare, and compensation of considerable matrix suppression/enhancement only had to be performed for certain samples. Besides mycotoxin determination and quantification, the presence of 18 different mold species was confirmed applying microbiological approaches in combination with macro- and microscopic identification according to DIN ISO 16000–17:2010–06. These results additionally highlight the diversity of mycotoxins potentially arising in indoor environments and leads to the assumption that indoor mycotoxin exposure stays an emerging topic of research, which has only just commenced.