Malt bagasse is the primary solid waste product from the brewing process, with notable environmental implications. Due to its nutritional value, it has potential as animal feed, primarily through ensilage. Alfalfa pellets can enhance this silage by adding digestible nitrogen and fibre. However, the high moisture content favours microbial contamination, particularly by fungi like Fusarium, which produces harmful mycotoxins. This study evaluated the impact of winter silage on fungal diversity, Fusarium presence, and mycotoxin contamination in malt bagasse, comparing the pre- and post-silage stages with the addition of alfalfa pellets. Results showed a diverse range of fungi, including Mucor, Cladosporium, Fusarium, and Penicillium, as well as yeasts. Fungal contamination was higher before silage, although the addition of alfalfa increased it after silage was produced. Fusarium verticillioides was the most common Fusarium species. Mycotoxin analysis detected DON (1.4 ppb) in only one sample. A two-month winter silage process under cold-temperate conditions appears to reduce fungal contamination and preserve feed quality. These findings support silage as a circular strategy to manage brewery waste safely, but further research and policy measures are needed to minimise biological risks in the brewing and livestock sectors amid climate change.