A collection of fourteen winter wheat accessions was evaluated to describe agro-morphological traits over a two-year study at four locations. Changes in grain yield, test weight, and plant height were related to differences in growing seasons, locations, genotypes, and their interactions. Thus, some genotypes are suitable for one location but not for another. However, a PCA showed that genotypes 2, 26, 28, 32, and 31 were the most stable across environments. In the 2022/2023 season, a negative relationship was observed between septoria leaf blotch, septoria nodorum blotch, yellow rust, fusarium head blight, and grain yield. Grain yield decreased by 84.8, 72.3, 37.4, and 4.3% in Kutjevo, Osijek, Tovarnik, and Zagreb, respectively, compared to the 2021/2022 season. Additionally, in the 2022/2023 season, barley yellow dwarf virus weakened wheat plants, especially at the locations Kutjevo, Tovarnik, and Osijek, where a relationship was observed with septoria leaf blotch and powdery mildew. At the Zagreb location, wheat genotypes were planted at the latest sowing date, probably escaping the virus pressure after plants easily tolerated diseases, resulting in a significantly higher mean grain yield.