The synthesis of late-maturity alpha-amylase (LMA) occurs when wheat experiences a cold-temperature ‘shock’ during the post-anthesis, grain-filling period. This markedly increases the high isoelectric point (pI) alpha-amylase in wheat grains in susceptible varieties. The affected grain has low Falling Numbers (FN) and is rejected at receival point or downgraded to feed grade, as low FN is associated with inferior end-product quality. However, several studies have reported the lack of correlation between low FN-LMA and end-product quality. Here, we characterize, for the first time, starch molecular structure and gelatinization properties of cold-treated wheat grains; starch structure has significant influence on flour functionality and end-product quality. Results show that the cold-treatment during post-anthesis has minimal effect on starch structure. While there was a small decrease in the gelatinization temperature for every wholemeal flour samples from cold-treated wheat grains, this is unlikely to cause any undesirable effect on end-product. The present findings suggest that the supposition that LMA is a major contributor to inferior end-product quality should be reconsidered.