In the perspective of cereal-based functional food development, the research compared stone watermill and stone mill which differed in the heating generated during grinding (30 and 60 °C) and the effects of storage on the preservation of phytochemicals. After 6-month storage of flour, a decrease in soluble dietary fibre (loss of 1.9–2.5 g 100 g−1) and bound polyphenols (loss of 6.2–8.5%) was observed, while other wheat grain components remained unvaried. Comparing the milling techniques, stoneground wheat grains (60 °C) showed the highest amylose (34.7–36.9% of total starch) and resistant starch amounts (0.85–1.16% of total starch), which could be of interest for lowering Glycaemic Index. Stoneground KAMUT® starch had higher tendency to be converted into resistant starch and it also showed the higher degree of starch damage, as compared to the durum wheat variety Claudio. The study provided suggestions for modulating the production chain with the aim of supplying added value to wheat-based products.