Different wheat species, common wheat (Triticum aestivum subsp. aestivum), spelt (Triticum aestivum subsp. spelta) and einkorn (Triticum monococcum subsp. monococcum), were analyzed for physicochemical (moisture, ash, protein, wet gluten, lipid, starch, carbohydrates, test weight and thousand-kernel mass) and mineral elements (Ca, Mg, K, Na, Zn, Fe, Mn and Cu) concentrations in grains. Additionally, wheat grain microstructure was determined using a scanning electron microscope. SEM micrographs of wheat grains show that einkorn has smaller type A starch granule diameters and more compact protein bonds compared to common wheat and spelt grains, making it easier to digest. The ancient wheat grains presented higher values for ash, protein, wet gluten and lipid content compared to the common wheat grains, whereas the carbohydrates and starch content were significantly (p < 0.05) lower. The mean values showed that spelt (Triticum aestivum subsp. spelta) grains presented the highest values for Ca, Mg and K, while einkorn (Triticum monococcum subsp. monococcum) grains had the highest values for the microelements Zn, Mn and Cu. The highest values of Fe were recorded for common wheat varieties whereas no significant differences among the species were obtained for Na content. The principal component analysis (p > 0.05) between wheat flours characteristics showed a close association between wheat grain species and between the chemical characteristics of gluten and protein content (r = 0.994), lipid and ash content (r = 0.952) and starch and carbohydrate content (r = 0.927), for which high positive significant correlations (p < 0.05) were obtained. Taking into account that Romania is the fourth largest wheat producer at the European level, this study is of great global importance. According to the results obtained, the ancient species have higher nutritional value from the point of view of chemical compounds and macro elements of minerals. This may be of great importance for consumers who demand bakery products with high nutritional quality.