Agronomic and seed-quality traits in 17 quinoa (Chenopodium quinoa Willd.) accessions grouped according to seed colour (i.e. ochre and yellow) were investigated and compared with the white commercial cultivar Regalona-Baer. These accessions were previously selected from a range of accessions of diverse origin and seed colour for their potential value in a breeding program for cultivars adapted to the southern Italian environment. Field trials were conducted over 2 years in Foggia, southern Italy. The aim was to identify elite genotypes suited to the Mediterranean Basin in terms of high yields and seed quality, by using principal component analysis (PCA) and hierarchical cluster analysis. The genotype and year effects were statistically significant for most parameters investigated, whereas the genotype × year interaction was significant only for seed quality. There were significant differences between the two seed-colour groups for most of the investigated traits, but not for total dry weight, days to flowering, and soluble and insoluble fibre. The major difference between the accessions and cv. Regalona-Baer was lower seed yield for the ochre seed group (30% lower, on average); this was associated with increased plant height (13% higher, on average), greater number of days to maturity ( 6 days, on average) and shorter panicle length (21% shorter, on average). These results were observed for both growing seasons. The seed yield of the yellow seed group was similar to Regalona-Baer. Focusing on individual accessions, PCA indicated that accessions Q12, Q18 and Q26 were similar to Regalona-Baer for seed yield, 1000-seed weight, seed area and seed perimeter, and accession Q4 had the highest protein and kaempferol contents for both years. Seed area and perimeter, harvest index, and 1000-seed weight showed positive associations with seed yield, whereas days to flowering, days to maturity and quality traits were negatively correlated with seed yield for both years. Cluster analysis carried out on all of the agronomic and seed-quality traits did not show clear clustering of the accessions based on seed colour alone. The results of this study confirm that both the ochre and yellow quinoa seed groups included elite accessions that can be used directly in future selection programs for the development of high-yielding varieties well adapted to the Mediterranean environment.