The present study investigates the biochemical responses of buckwheat to drought stress, particularly focusing on phenolic acids and flavonoids, abundant in this crop. We hypothesize that distinct genotypic responses to drought stress will lead to variations in phenolic acid accumulation. Two common buckwheat cultivars, Panda (East European origin) and PI 482597 (originating from Zimbabwe), were subjected to drought treatment, with biochemical traits, relative water content, and photosynthetic pigments regularly assessed. While chlorophyll content remained unaffected by dehydration, total carotenoid content decreased. The unique increase in the chlorophyll to carotenoid ratio suggests a specific role of carotenoids in buckwheat's metabolic stress response. While most phenolic acids and flavonoids exhibited increasing trends during progressive dehydration, their dynamics differed. Notably, rutin content increased early in drought stress, while chlorogenic acid and kaempferol showed enhanced levels only under severe dehydration. Genotypic differences were observed in chlorogenic acid, neochlorogenic acid, cryptochlorogenic acid, 4-hydroxybenzoic acid, and quercetin. Conversely, trans-p-coumaric acid, trans-ferulic acid, vanillic acid, rutin, and kaempferol showed similar trends in both cultivars. By aligning observed drought-induced changes in phenolic compound contents with biosynthesis pathways, trade-offs between individual compounds were identified, contributing to the mechanistic understanding of varied stress responses.