We performed field trials with a diversity panel of 350 quinoa accessions. The accessions displayed large phenotypic variation with regard to flowering time and other agronomically important traits. All the accessions of the diversity panel were sequenced by a whole-genome re-sequencing approach. We obtained ~3 million high-quality SNPs, which we used to identify significant associations between SNPs and important traits, such as flowering time, panicle length, plant height, saponin content, thousand kernel weight (TKW), and seed yield, and to identify putative candidate genes for agronomically important traits. We aim to use sequence variations to select promising accessions as crossing partners to breed new varieties well adapted to European climate conditions.Overall, our study provides resources for fast track genetic improvement of the underutilized pseudocereal quinoa. This will enable harnessing its undiscovered potential in sustainable agricultural production and its adaptation to new environmental conditions.