To combat climate change and environmental pollution, agriculture must reduce mineral fertilizer use and adopt sustainable, low-input, and organic practices. In such systems, plants depend on the soil microbiome for nutrient acquisition and growth. Thus, enhancing plant-microbiome interactions is vital for maintaining or even increasing production sustainably. Modern plant breeding has led to barley cultivars that yield high under substantial mineral fertilizer application. However, this selective breeding may have diminished traits essential for plant-microbiome interactions, making these cultivars less suitable for sustainable agriculture. In contrast, older cultivars might have preserved traits from their common wild ancestor, enabling them to prosper under low nutrient conditions. This study evaluated four modern elite barley cultivars and three older (pre-1980). Grown under various fertilizer regimes, we assessed their root microbiome using 16S rRNA amplicon sequencing. Our objectives were: i) to determine the impact of nutrient availability on plant nutrient uptake and biomass production, and ii) to understand how the time since domestication (domestication age), individual cultivar, and fertilizer regime influence the root microbiome. We found that without fertilizer, old cultivars had superior biomass production and higher leaf concentrations of nitrogen, potassium, sulfur, iron, zinc, and copper than modern cultivars. This indicates that older barley cultivars may have retained their wild ancestors' capability to synergize with the soil microbiome, enhancing nutrient acquisition in low-input systems. Notably, the diversity of the rhizo-microbiome was not significantly affected by domestication age but varied with individual cultivar and fertilizer treatment.