The need for foods with high nutritional value has led to the rediscovery of ancient wheat species Triticum sphaerococcum and T. persicum as raw materials with valuable consumption properties, but their reintroduction requires assessment of their productivity under different agricultural practices. The field experiments were carried out for three years (2018–2020) to test the hypothesis that the sowing density of T. sphaerococcum and T. persicum (400, 500 and 600 no m−2) will affect their agronomic traits, yield and occurrence of diseases, but the response will depend on the hydrothermal conditions of the growing seasons. In this study, a significant correlation of the grain yield with the amount of precipitation in tillering, and from booting to the beginning of fruit development was demonstrated. The sowing density of T. sphaerococcum had an impact on the grain yield only under moderate drought stress during the growing season (2019), when the highest yield was obtained at a sowing density of 600 m−2. In 2019, the most favorable sowing density was also the highest for T. persicum. In the year with the lowest amount of rainfall during the growing season (2018), the yield of T. persicum was the highest in the lowest sowing density. At the shooting stage, a greater intensity of powdery mildew was observed on T. persicum, especially with higher sowing densities. Increasing the sowing density also increased the occurrence of root rot symptoms in both wheat species in the year that favored the occurrence of this disease (2018). It can be concluded that in the integrated low-input cultivation of T. sphaerococcum and T. persicum, it is justified to use a sowing density of 600 pcs. m−2, in an agroclimatic zone with moderate droughts during the growing season.