The global production of quinoa has been increasing in recent years. In plant-based foods, ultrasound stress has received increasing attention, owing to its ability to enhance the production of primary and secondary metabolites. We studied the effects of ultrasonic stress at the pre-germination stage on the γ-aminobutyric acid (GABA) accumulation and characteristics of nutrition and function in quinoa. The results showed that ultrasonic conditions of 100 W for 4 min promoted an increase in GABA content by 9.15-fold, to 162.47 ± 6.69 mg/100 g·DW, compared to that of untreated quinoa, through promoting a 10.2% and 71.9% increase in the water absorption and glutamate decarboxylase activity of quinoa, respectively. Meanwhile, compared to untreated quinoa, ultrasonic stress at the pre-germination stage enhanced the total phenolic, total flavonoid, and total saponin contents of quinoa by 10.2%, 33.6%, and 90.7%, to 3.29 mg GA/g·DW, 104.0 mg RE/100 g·DW, and 7.13 mg/g, respectively, without decreasing its basic nutritional quality. Ultrasonic stress caused fissures on the surface of quinoa starch particles. Additionally, germination under ultrasonic stress increased the n3 polyunsaturated fatty acids by 14.4%. Furthermore, ultrasonic stress at the pre-germination stage promoted the scavenging of 2,2-diphenyl1-picrylhydrazyl radicals and inhibitions of α-amylase, α-glucosidase, and pancreatic lipase by 14.4%, 14.9%, 24.6%, and 20.0% in vitro, compared to untreated quinoa. The results indicated that the quinoa sprouted via ultrasonic stress could represent a promising method through which to develop nutritionally balanced whole grains rich in GABA, with hypoglycemic and hypolipidemic activities, which could provide theoretical support for the development of functional whole-grain foods based on quinoa.