The use of Fusarium-infected barley for malting and brewing can lead to mycotoxin production and result in decreased malt quality. Chemical methods for treatment of Fusarium-infected barley may be effective in preventing these safety and quality defects and allow use of otherwise good quality barley. In this study, micro-malting experiments were conducted using peracetic acid (PAA) to evaluate effectiveness in reducing Fusarium survival and associated production of the mycotoxin deoxynivalenol (DON) while maintaining germinative energy in barley. Addition of PAA to the steep water was effective in reducing both the infection rate and vitality of Fusarium on barley. The magnitude of the antifungal effect of PAA was dependent on both concentration and contact time. The treatments were less effective in reducing the rate and viability of Fusarium when the pH was modified to 9.0. PAA treatment of the steep water was effective at reducing DON levels in finished malt. Germination characteristics of the grain were significantly impaired by PAA at concentrations as low as 290 ppm when included in the steep water. Reductions in germination were not as severe when pH was modified to 9.0. The results of the study suggest that PAA may have potential for treatment of Fusarium-infected malting barley without detrimental effects on germination, especially when used as a short first immersion (rinse).