Lactoperoxidase is an enzyme that generates oxidants with antimicrobial activity in presence of a (pseudo)halogen and hydrogen peroxide, but various factors can drastically reduce the antimicrobial activity of the lactoperoxidase system. Spectroscopic, ionic chromatography, and 13C-NMR methods showed that the oxidants generated by lactoperoxidase are OSCN− in the presence of SCN− and I2 in the presence of I−. Neither of them, however, inhibited Penicillium expansum, one of the causal agents of fruit mold. When a mixture of SCN− and I− was used, no OSCN−, OCN−, I2, or interhalogen I2SCN− was produced. However, its long-term stability, NH2-oxidizing capacity, and antifungal activity against P. expansum argue in favor of an I−-derived oxidant. Strongly mineralized water optimized enzyme-catalyzed reactions with higher oxidant production. Storage at 4 °C resulted in long-term stability and extended antifungal activity against P. expansum. The relative iodide/thiocyanate concentrations turned out to be important, as better in vitro inhibition of Botrytis cinerea, the causal agent of apples’s grey mold, was obtained with a high KI + KSCN concentration, a KI/KSCN ratio of 4.5, and a (KI + KSCN)/H2O2 ratio of 1. The nature of the substrates, their relative concentrations, the medium, and the storage temperature modifed the antifungal activity of lactoperoxidase.