The present work evaluated the physicochemical and functional characteristics of different indigenous buckwheat varieties grown in Gilgit Baltistan, Pakistan, using grains and milled flour (fine flour, coarse flour, bran, and husk). Results showed that the thousand grain weight, length, width, thickness, arithmetic mean diameter, and geometric mean diameter were found to be highest in common buckwheat. In contrast, the highest mean values for sphericity were observed in Tartary buckwheat. The water absorption capacity, oil absorption capacity, swelling capacity, foaming, and foaming stability were high in common buckwheat as compared to Tartary buckwheat. Results regarding chemical properties revealed that common buckwheat contained higher quantity of protein (14.67%), fat (3.86%), fibre (1.38%), ash (2.24%), and total carbohydrate (65.8%); while Tartary buckwheat contained moisture (13.31%), protein (11.9%), fibre (1.38%), fat (3.57%), ash (2.69%), and total carbohydrate (68.8%). Furthermore, during the comparison of milling factions, it was found that buckwheat husk contained the highest quantity of copper (6.78 mg/100 g) and manganese (32.79 mg/100 g), while fine flour proved to be a rich source of magnesium. The present work identified variability among buckwheat varieties and milling fractions for physicochemical and nutritional traits that could be used to supplement various food products as functional ingredients.