The study of effects of Ca2+ and Mg2+ on antifungal activity of lactic acid bacteria (LAB) isolates and their associations revealed inducing and inhibiting effects on antifungal activity. The addition of Ca2+ essentially inhibited the antifungal effect of L. rhamnosus MDC9661 but stimulated the activity of RIN-2003-Ls, MDC9632 and MDC9633 strains, as well as their associations. Mg2+ partly increased the inhibitory activity of LAB isolates, while the addition of ions combination did not cause changes of their antifungal activity. The supplementation of Ca2+ stimulated the antifungal effect of most associations against Penicillium sp., Trichoderma viride, Geotrichum candidum, and Aspergillus flavus compared with the native conditions. The addition of Mg2+ induced the antifungal activity of RIN-2003-Ls, MDC9632, MDC9633, and INR-2010-Tsov-G-St combinations. The antifungal effects of most associations were increased in the presence of ions mixture. The natural LAB associations including VKPM B-3386, MDC9632, and MDC9633 could not suppress the growth of any tested mold; however, the supplementation of ions combination revealed their antifungal effect against all kinds of molds. The finding of substantial stimulation of the most LAB associations antifungal effect by metal ions can be basis for creation of new effective antifungal preparations by the supplementation of ions combined mixture.