Fungal diseases are a yield-limiting factor for wheat. Their management in organic production systems is one of the prevailing challenges because it must be based mainly on indirect measures through agricultural practices. Variety mixtures are one of these practices, a concept that has been demonstrated to improve several factors affecting yield. Recently, it has become a practice that enables sustainability in agriculture. Our research aim is to evaluate the capacity of this practice to control three fungal diseases (foliar and ear) on durum wheat. This study was conducted over two consecutive years (2019 and 2020) at two locations: a certified organic farm in the Benslimane region (2019) and the National School of Agriculture farm in Meknes (2020). Four durum wheat varieties (Isly, Tarek, Karim, and Nassira) were used to create the mixture. The parameters that were monitored were the disease severity, the grain yield, and its components. The analysis of variance for the three fungal diseases’ severity was significant. The variety that showed resistance to all diseases was the Isly variety, and the most susceptible variety was the Nassira variety. The resistance of the other varieties to the diseases was variable from one year to the other. The mixture showed average severity values. It allowed a reduction in the severity of leaf rust of 47% during the first year and 30% during the second year compared to the most susceptible variety (Nassira). In the case of HLB (helminthosporiosis leaf blight), it reduced the disease by 47% during the first year and 34% during the 2020 season. For ear disease, Fusarium head blight (FHB), the reduction was 68% during the year 2019 and 49% during 2020. The mixture also ensured yield stability between the two trial years (1.66 t ha−1 and 1.54 t ha−1).