In industrial malting, the temperature of the grain bed is difficult to control during the air-rest periods in steeping, and high temperatures during steeping may lead to high malting losses and impaired malt quality. Nitrogen gas was applied during air rest with the aim of controlling heat production in pilot-scale malting. This procedure was compared to air recirculation and continuous aeration. Nitrogen gas efficiently restricted heat formation and had a negligible effect on malt quality, although it did delay germination. In addition, nitrogen gas was applied at the beginning of kilning to suppress fungal growth and improve malt quality. When nitrogen gas was applied during kilning, Fusarium levels and lipoxygenase activity in malt decreased significantly, whereas endopeptidase and limit dextrinase activities increased. Based on these results, the application of nitrogen gas during malting offers a potential means of tailoring malt quality.