Fusarium head blight (FHB) is a devastating disease of barley that leads to significant losses for the malting and brewing industry; however, there has been insufficient attention towards understanding the new fungal growth and the production of deoxynivalenol mycotoxin during the malting process. Field trials were carried out in 2019, 2020 and 2021 at Agriculture and Agri-Food Canada-Brandon Research and Development Centre, Brandon, MB. Barley varieties of different FHB resistant levels: Newdale (moderately resistant to moderately susceptible) and AAC Goldman (moderately resistant) were inoculated with single strain conidial suspensions of each of seven different Fusarium graminearum strains, plus a non-inoculated control. The severity of FHB (as a percentage of visibly symptomatic spikelets) was higher in Newdale than in AAC Goldman in all three years of the study (9% vs. 3%, respectively in 2019; 38% vs. 21% in 2020; 3.5% vs. 0.6% in 2021). FHB in non-inoculated controls was present at low levels compared to inoculated treatments each year. Cultivar differences were also evident and consistent across years when Fusarium density was assessed by quantitative PCR (Fusarium: barley gene abundance ratios averaged 74.3 in Newdale vs. 36.5 in AAC Goldman in 2019; 9.7 vs. 4.4 in 2020; 22.1 vs. 13.9 in 2021) and in non-inoculated controls, the Fusarium density was at very low levels. Deoxynivalenol content (determined via ELISA) in the harvested grain was also higher in Newdale than in AAC Goldman (11.6 vs. 5.0 ppm in 2019; 1.2 vs 0.7 ppm in 2020). We micro-malted this Fusarium-infested barley and found that cultivar differences in susceptibility factors persisted through malting; Fusarium density in finished malt remained higher in Newdale than in AAC Goldman (17.0 vs. 12.4 in 2019; 4.3 vs. 2.1 in 2020; 19.0 vs. 18.2 in 2021), as did deoxynivalenol content in the finished malt (3.8 ppm in Newdale vs. 1.4 ppm in AAC Goldman for 2019). Both Fusarium density and deoxynivalenol content were significantly correlated between barley and finished malt (P < 0.05). Differences among Fusarium strains were less frequent than expected, although in general deoxynivalenol content was higher for pathogen strains with a 3-acetyl-deoxynivalenol chemotype, compared to those with a 15-acetyl-deoxynivalenol chemotype. Future study objectives will be to understand the relationship between Fusarium trait variability and malt quality parameters which will suggest more effective criteria for grading barley grain or predicting final quality at early stages of malting.