Wheat (<em>Triticum</em> <em>aestivum</em> L.) is pivotal to global food security, with its energy-rich grains that are also the major vegetable protein source in human diets. Decades of primary emphasis on grain yield improvement have delivered increased gains worldwide, but the grain protein content has declined. Since amino acids are biosynthetic precursors of proteins, this research hypothesized that their contents in the wholegrain flour have also been impacted by past wheat breeding. To test this, the free amino acid content of wholegrain flour in 92 wheat cultivars released in a 20-year period were analyzed by regression against the year of release. The slope of the regression showed positive increases per year in 16 of the 19 individual amino acid considered. Among these, the increases in lysine, aspartic acid and arginine were statistically significant (P < 0.05). The level of lysine in wholegrain flour increased by 0.30 mg kg<sup>-1</sup> yr<sup>-1</sup> (R<sup>2</sup> = 0.24) over the 20-year period of breeding. Similarly, the content of methionine increased by 0.2 mg kg<sup>-1</sup> yr<sup>-1</sup> (P = 0.07; R<sup>2</sup> = 0.16), but free asparagine also increased at the rate of 6.51 mg kg<sup>-1</sup> yr<sup>-1</sup> (P = 0.11; R<sup>2</sup> = 0.13). The study sought further to explore the impact of selection for key developmental genes (<em>Vrn</em>, <em>Ppd</em>, and <em>Rht</em>) that have been targeted for artificial selection since 1840. Wheat cultivars carrying the semi-dwarfing gene, <em>Rht-B1b</em>, showed 15% lower content of lysine (the most limiting essential amino acid) and 25% lower content of free asparagine (precursor of the neurotoxin, acrylamide) in the wholegrain compared to the tall cultivars. At the <em>Vrn-A1</em> gene, the winter-type cultivars carrying <em>Vrn-A1v</em> allele were 28% lower in free asparagine, and 6% lower in lysine content than their spring-type (<em>Vrn-A1a</em>) counterparts. In conclusion, the results indicated that, contrary to the declining trend in grain protein content, free amino acids in wheat wholegrain flour have been increased by past breeding. Selections for semi-dwarfism and vernalization response have had significant impacts on free amino acid content, implying that genetic manipulation of <em>Rht-B1b</em> and <em>Vrn-A1</em> genes could present a pathway to reducing the acrylamide-forming precursor in wheat wholegrain flour.