AbstractGenetic and environmental factors influence wheat grain quality, including vitreousness, protein, and starch content. Yellow berry (YB), a physiological condition, adversely affects wheat quality, particularly in irrigated fields with limited nitrogen application, leading to starch‐rich, low‐protein grains. This study examines common wheat, used in baking industries, and durum wheat, primarily employs for pasta production. The focus is on investigating how the physicochemical properties of these wheat types change with the presence of YB, that impacts protein content negatively, increasing total starch content. Fourier‐transform infrared spectroscopy reveals structural changes in YB‐affected grains, while X‐ray diffraction indicates varying crystallinity. In determination of amylose, an increase of 6% in bread wheat with YB and 3% in durum wheat with YB is observed. In the case of RVA (Rapid Visco Analyzer) analysis, a notable increase in viscosity is evident in the treatments that included the yellow berry. This finding suggests that YB is associated with substantial modifications in starch properties, such as amylose‐to‐amylopectin ratio, chain length, and degree of branching, among several other components, which may have important implications for the texture and quality of food products. This study calls for further research to mitigate YB's impact and enhances the quality of wheat‐derived foods.