The primary bioactive components of buckwheat seeds, rutin, and quercetin, have health-related benefits such as anti-inflammatory, antioxidant, anti-diabetic, and anti-cancerous. In the current study, we characterized the agro-morphological traits of diverse tartary buckwheat germplasm accessions under the spring cultivation and estimated the major flavonoid contents of seeds. The content of rutin and quercetin ranged from 4354.1 to 17,196.01 and 8.9 to 611.7 µg g⁻¹ DW, respectively. The highest content of rutin was found in ‘C9714’ collected from China. The highest and lowest content of quercetin was found in Indian accessions ‘I8345’ and ‘I8622’, respectively. Moreover, we found that accessions with dark-brown seed coat color had a significantly higher mean rutin content than that of accessions with other seed coat color. In the principal component analysis, the first three components (PC1, PC2, and PC3) accounted for 77.14% of the total variation. The number of nodes and branches, number of days to flower, and maturity were the main contributors of variability to PC1. The 1000-seed weight was the main contributor of variability to PC2; whereas, the rutin and quercetin were the main contributors of variation to PC3. We identified nine accessions with the rutin content above 10,000 µg g⁻¹ DW and three accessions with quercetin content above 40 µg g⁻¹ DW. The selected accessions could be used as a nutritional source of health-related bioactive metabolites.