The pathogenic fungus Puccinia graminis f. sp. tritici is the cause of wheat stem rust. Twenty bread wheat varieties were assessed in the current study, between 2020 and 2022 based on the final rust severity (FRS %) and the area under disease progress curve (AUDPC). Over the course of the three seasons, the Misr-1 variety registered the greatest disease parameters (FRS% and AUDPC). The estimation of losses in the Misr-1 variety at varying infection levels (0–100%) and their relationship to the physicochemical and technological properties of wheat flour were the main objective of this study. Compared with zero and 20% infection levels, estimated and actual losses (%) for 1000 kernel weight and yield/feddan were highest at 80 and 100% of the infection. A significant positive correlation was found between the degree of infection and the actual loss (%) of both1000 kernel weight and yield/feddan (ardab). The physicochemical characteristics of the wheat flour (82% extraction rate) extracted from the Misr-1 wheat variety at different level of stem rust revealed significant different values for 1000 kernel weight, moisture, protein, fat, and total carbohydrates contents, meanwhile no significant difference in the ash and crude fiber contents. The hectoliter weight and flour extraction rate decreased from 83.24 to 80.14 Kg/hl and from 65 to 61%, respectively, as the infection level increased from zero to 100%. Moreover, there was a significant decrease in wet gluten, dry gluten, gluten index, and hydration ratio as the infection level increased. As well as the infection levels increased from zero to 100%, the wet and dry gluten content declined from 31.13 to 30.08% and from 10.08% to 9.88%, respectively. Concerning the rheological properties, the rust infection significantly lowered the water absorption (WA) as well as the dough development time (DDT) and dough stability time (DST) of the wheat flour. Finally, all sensory parameters of the produced balady bread, showed no significant changes, with the exception of appearance and layer separation scores, which significantly declined from 8.85 to 8.15 and from 8.85 to 8.30, respectively. This may be due to the lowering gluten content and hydration ratio.