Background and objectives Consumption of whole grain cereal products, which are rich in phenolic acids, is associated with lower risk of degenerative diseases. Phenolics in plants are associated with abiotic stress adaptation due to their antioxidant activities. Free, bound, and total phenolics in the wholemeal flour of 50 durum wheat (Triticum turgidum L. ssp. durum) genotypes were examined, in addition to the water stress tolerance capacity of selected genotypes. Findings This study revealed significant variation, with wholemeal flour from “Purple Grain” having the highest total phenolic content (391.0 mg gallic acid equivalent per 100 g of dry weight [GAE/100 g DW]). Under water‐deficit stress, the stress‐tolerant genotype Tamaroi had higher total phenolic content in the leaf (2880.3 mg GAE/100 g DW) compared to stress‐sensitive genotypes EGA Bellaroi and Tjilkuri (2292.6 and 2450.1 mg GAE/100 g DW, respectively). In the mature grains, stress‐tolerant genotypes Tamaroi and Yawa had significantly higher total phenolic content under stress compared to the control, while no significant change was found in the stress‐sensitive genotypes EGA Bellaroi and Tjilkuri. Conclusions Results suggest that phenolic content could be associated with water‐deficit stress tolerance. Significance and novelty Selected genotypes could now be used as parents for breeding varieties with increased phenolics and stress tolerance capacity.