The morphological effects of an antifungal activity produced by Lactobacillus plantarum 16, a malt-production steep water isolate, on two food-associated fungi were examined microscopically. Spore germination was completely inhibited in Aspergillus fumigatus and Rhizopus stolonifer upon treatment with concentrated cell-free supernatant (cCFS) of strain 16. Furthermore, addition of antifungal cCFS to germ tubes and hyphae halted further development compared to untreated controls. Transcriptome analysis of A. fumigatus Af293 following exposure to antifungal cCFS revealed a number of genes with altered transcription involved in a variety of cellular functions, most notably cell metabolism, suggesting a global metabolic shutdown and subsequent cell death. Increased transcription of the global regulator LaeA was also observed indicating that exposure to the antifungal activity caused a cellular stress response.