The Weissella genus has recently gained popularity due to its antifungal and probiotic properties. In this study, the antifungal activity of isolate KM14 of Weissella cibaria on Aspergillus fumigatus, Penicillium expansum, and P. oxalicum were evaluated by the overlay method and microplate inhibition analysis; results showed that the bacterium had a high inhibition rate against these three fungi, ranging from 99.4 to 94.3%. The evaluation of the antifungal activity of compounds (organic acid/proteins/H2O2) produced by the bacterium revealed that organic acids were responsible for this activity. As observed by scanning electron microscopy (SEM), shrunken hyphae and pores on the cell surface were observed in cell free supernatant (CFS)-treated fungi. The predominant organic acids identified in the CFS were lactic acid and acetic acid, respectively. Furthermore, the genome of W. cibaria KM14 contained a significant number of genes (130) that were responsible for organic acid biosynthesis. Based on these data, it has been speculated that W. cibaria KM14-CFS inhibits fungal growth via two potential mechanisms: decreasing hyphal surface decoration and damaging the mycelia.