Quinoa is a resilient crop known for its adaptability to diverse environmental conditions. This study examined the agronomic performance and ecological adaptability of quinoa across four distinct altitudes in the northwestern regions of China. Six quinoa genotypes were assessed for agronomic traits, phenology and yield performances, and nutritional quality characteristics in Yining city, Nilka County, Tekes County and Zhaosu County under varied environmental conditions. Our findings demonstrate significant variations in all measured traits, including agronomic and nutritional quality traits, across the various altitudes and genotypes. In Yining city, a warmer and lower altitude area, genotypes exhibit superior traits for fodder production, including increased branches, longer panicles, robust stems, and high seed protein content. Genotypes Jinli 1 and Beijing 2 achieve yields exceeding 3 tons per hectare (t/ha), highlighting the region’s productivity. The Nilka and Tekes counties boasted the shortest quinoa crop cycles, with Jinli 1 yielding 4.05 t/ha seeds in Tekes County, exhibiting high protein and fat content alongside low saponins, making it a prime location for yield production. Zhaosu County, with its cooler climate and fertile chernozem soil, elicited high 1000 seed weight and more robust protein response than Nilka and Tekes counties, illustrating the impact of soil fertility on nutritional composition. Correlation analyses further elucidated that the plants characterized by shorter flowering times, crop cycles, compact inflorescence, and taller heights exhibited superior seed yields. Our study contributes significant insights into the ecological adaptability and nutritional dynamics of quinoa, with implications for sustainable crop production and food security in diverse agroecosystems.