One of the major challenges in agriculture is the loss of productivity in bread and durum wheat genotypes cultivated in Azerbaijan due to water scarcity. As a result, the development of wheat genotypes that are resistant to both abiotic and biotic stresses remains a key focus of research. This study examined the effect of drought stress on the activity of key metabolic enzymes-phosphoenolpyruvate carboxylase (PEPC), aspartate aminotransferase (AspAT), and NAD-malate dehydrogenase (NAD-MDH) in durum and bread wheat genotypes during the milky stage (MS), dough stage (WS), and physiological stage (PS) of grain development. Results indicated that PEPC activity significantly increased during the WR stage in the drought-tolerant durum wheat variety Barakatli 95, showing a threefold increase under drought conditions. In contrast, the drought-sensitive Garagylchyg 2 exhibited a smaller increase of 1.5 times. In bread wheat varieties, PEPC activity remained unchanged in Tale 38, while it decreased by twofold in the ripening seeds of the drought-sensitive variety Gobustan in the dough stage. AspAT activity was stable in durum wheat but significantly decreased in bread wheat, particularly in the Gobustan variety. NAD-MDH activity increased in durum wheat, while it decreased in bread wheat under drought conditions. Further biochemical studies on sensitive and tolerant wheat varieties could provide valuable insights into drought tolerance and help identify promising genotypes for future breeding programs.