The antioxidant activity and content of bioactive substances, including γ- aminobutyric acid, epicatechin, epigallocatechin gallate, saponins and polyphenols, in black quinoa, red quinoa and white quinoa were studied in this study. The results showed that, after 72 h germination treatment, the content of γ-aminobutyric acid in black, red and white quinoa increased to 110.10, 157.40 and 135.70 mg/100 g at maximum, respectively. The increase rate of the epicatechin was the biggest, and they were found to be 7.11, 5.32 and 1.32 times, respectively. Among which, the content of epigallocatechin gallate increased by 4.23, 2.79 and 3.29 times, respectively. In addition, the saponins content and total polyphenols content of the three kinds of quinoa increased with the prolongation of germination time. The increase of DPPH clearance rate and iron ion reducing ability indicated that germination could improve the antioxidant activity of quinoa in vitro. The results showed that the content of beneficial bioactive substances and antioxidant capacity of quinoa could be effectively improved by germination treatment.