Fumitremorgin C and verruculogen are mycotoxins produced by heat-resistant Neosartorya fischeri. Easy and fast monitoring of their production by selective and sensitive analytical methods is crucial for ensuring postharvest quality of fruit, food safety, and thus human health and well-being. A six-minute liquid chromatography tandem mass spectrometry method (LC/MS/MS) was developed for quantification of fumitremorgin C and verruculogen in potato dextrose broth (PDB), strawberry juice, strawberry fruit, and soil. Mycotoxins were extracted from all media with the QuEChERS (Quick Easy Cheap Effective Rugged Safe) method. The lower limit of quantification (LLOQ) of the method for both mycotoxins was 1 μg L−1 for PDB and strawberry juice and 1 μg kg−1 for strawberry fruit and soil. Collision-induced dissociation of protonated fumitremorgin C and verruculogen ions was also examined by high-resolution mass spectrometry to assist researchers in non-targeted screening for mycotoxins and in identification of these two toxins. The developed LC/MS/MS method was applied to examine mycotoxin production by 45 environmental Neosartorya strains: 5 well-known strains, included in the study as reference strains, and 40 strains that were newly isolated and identified by us.