Waxy wheat with low amylose content leads to reduced total starch production, grain size, weight, and yield compared to regular bread wheat. Proteomic and phosphoproteomic analyses of starch granule-binding proteins in waxy and non-waxy wheats showed that amylose reduction does not affect amylopectin synthesis but impacts overall starch biosynthesis. Different proteins involved in amylopectin synthesis have similar expression patterns, suggesting separate pathways for amylose and amylopectin production. Phosphoproteome analysis revealed that the lack of amylose does not affect the expression and phosphorylation of proteins related to amylopectin biosynthesis.