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A clear gap with respect to the potential biological properties of wheat flavonoids exists in the available literature. This information is crucial for breeding programs aiming to produce new varieties presenting improved health benefits. Accordingly, advanced breeding lines of whole durum wheat were evaluated in this contribution. The highest recovery of phenolics was achieved using aqueous acetone (50:50, v/v), as verified by multi-response optimization, thus showing that phenolics could be largely underestimated by employing an inappropriate extraction. The concentration of derivatives of apigenin, the main phenolics present, ranged from 63.5 to 80.7%, as evaluated by LC–ESI-QTOF-MS. Phenolics from the breeding line 98 exhibited the highest ability in scavenging peroxyl radicals, reducing power as well as in terms of inhibition of pancreatic lipase activity, a key enzyme regulating the absorption of triacylglycerols. In contrast, none of the samples exhibited a significant anti-diabetic potential. Despite their high concentration compared to that of phenolic acids, results of this work do not support a significant antioxidant and pancreatic lipase inhibitory effect of durum wheat flavonoids. Therefore, breeding programs and animal and/or human trials related to the effect of durum wheat flavonoids on oxidative stress and absorption of triacylglycerols are discouraged at this point.