In the north and center of Chile, there has been a significant environmental contamination by copper due to natural factors, mining activities and use of agricultural fertilizers and pesticides. Copper (Cu) soil contamination is of important concern in agriculture, food safety, and human health. Soil copper concentrations higher than 100-150 mg/kg can be toxic for plants and other organisms. Therefore, identification of copper-tolerant crops is of great interest for sustainable cultivation purposes. Quinoa is a promising candidate as a copper-tolerant crop, owing to its wide genetic diversity, high adaptability to different environmental conditions, and tolerance to abiotic stresses. In this work, we evaluated the effect of copper on 21 accessions of quinoa (including 19 accessions from different geographical locations of Chile) in order to identify tolerant and sensitive accessions. Our results show that (1) Germination parameters of quinoa are negatively affected in the presence of increasing Cu concentrations, with differential inhibition values among accessions. (2) Early seedling growth of accessions was differentially affected in the presence of Cu. (3) Plant biomass production (relative fresh and dry weights) was also affected by Cu, with significant differences between accessions. A Principal Component Analysis (PCA) of these data identified accessions based on Cu tolerance. (4) A clear regional pattern was observed when comparing accessions from northern, central, and southern Chile, suggesting local adaptation to Cu-rich soils. Thus, significant differences in copper tolerance between accessions were observed, revealing genetic diversity in copper tolerance among quinoa accessions. Tolerant accessions of quinoa can have important applications in sustainable agriculture.