Kiwicha (Amaranthus caudatus) is an Andean grain with an excellent nutritional value. Kiwicha is used to make different food products including breads and biscuits. However, little is known on the effect of germination process on bioactive compounds and functional properties of kiwicha. The objective was to maximize the content of gamma-aminobutyric acid (GABA), total phenolic compounds (TPC) and antioxidant activity (oxygen radical absorbance capacity, ORAC) of kiwicha sprouts through optimization of germination process. Optimization was carried out using Response Surface Methodology (RSM) with a 22 central composite rotational design. The independent variables studied were: germination time (12, 21, 42, 63 and 72 h) and germination temperature (12, 14, 20, 26, 28°C). The GABA and TPC content and antioxidant activity of the non-germinated kiwicha was 2.6 mg GABA/100g, 94.75 mg GAE/100g and 393.14 mg TE/100g, respectively. In general, levels of GABA, TPC and antioxidant activity increased significantly (P≤0.05) with longer germination times and higher temperatures. The optimal germination conditions were 26°C and 63 in which GABA, TPC and antioxidant activity increased 29.1, 4.0 and 6.4-fold, respectively. The phenolic composition was studied by HPLC-DAD-ESI/MS in those kiwicha sprouts obtained in the optimal conditions. These sprouts presented mainly non-flavonoids compounds, being hydroxycinnamic quinic acid derivatives (4-O-caffeoylquinic, 4-O-feruloylquinic acids) the most abundant and found only in sprouts. Quercetin-3-O-rutinoside was the only flavanol identified in kiwicha seeds, and an increased content of this compound was found in sprouts. In conclusion, germination is an effective process to improve levels of bioactive compounds and health promoting potential of kiwicha. Therefore, consumption of kiwicha sprouts as fresh foods or inclusion of germinated kiwicha flour in bakery products could help in the prevention of chronic diseases and malnutrition.