The aim of the study was to determine the antioxidant activity, total phenolic content, and total carotenoid content of dried fruit extracts prepared from goji fruits, cranberries, and raisins. Ergosterol content of samples-as a marker of fungal contamination-was measured by LC-MS/MS technique. For the goji fruit samples, fungal community-level physiological profiling and fungal isolate catabolic diversity were tested to evaluate more precisely their fungal contamination. The highest antioxidant activity and total phenolic content were determined for dried goji fruits. Simultaneously, the dried goji fruits were contaminated by ergosterol − 3.8 µg g −1 of dried fruit and the bulk goji fruits were contaminated by heat-resistant fungi. The study of fungal community as a fungal contamination marker of dried goji fruits was performed by a combination of the Biolog FF plates and traditional culture methods which is the first application of this composite analytical approach. Ergosterol content could be an indicator of fungal growth on dried fruits. The Biolog FF microplates can be used as a quick, easy, cheap, and effective method for the detection of heat-resistant fungi in dried fruits.