Background: Quinoa (Chenopodium quinoa Willd.), valued as a nutrient-dense grain, has seen expanded cultivation in China. However, its yield and quality are often unstable due to suboptimal fertilization practices, and the specific regulatory roles of macronutrients (N, P, K) remain unclear. This study aimed to elucidate the effects of combined NPK fertilization on the growth, yield, and nutritional quality of quinoa. Methods: A pot experiment was conducted in a controlled climate chamber using the “Jingli 1” cultivar. Plants were subjected to four fertilization treatments: NPK, PK, NK, and NP. Results: The NPK treatment significantly enhanced growth throughout the development cycle, increasing total root length (45.0±8.5%), root surface area (32.8±6.2%), plant height (20.0±5.0 cm), and dry matter accumulation (71.6±15.3%). It also improved nitrogen use efficiency and key yield components, including panicle length (5.63±1.22 cm), thousand-grain weight (0.34±0.02 g), and grain weight per plant (1.41±0.23 g). Nutritionally, the NPK treatment elevated the content of essential amino acids (284.10±52.75 mg/g), total free amino acids (2414.65±428.30 mg/g), and increased levels of protein, starch, and fat. Deficiency analyses revealed distinct limitations: nitrogen deficiency primarily constrained aboveground growth and yield; phosphorus deficiency strongly inhibited root development and dry matter accumulation; while potassium deficiency had comparatively minor effects. The synergistic application of NPK fertilizers is crucial for optimizing quinoa production. It promotes robust root and shoot growth, enhances nitrogen uptake, and simultaneously achieves high yield and superior nutritional quality, providing a scientific basis for optimized quinoa cultivation practices.