This study determined the content of macronutrients and micronutrients to investigate the nutritional value and health benefits of six varieties of quinoa seeds and sprouts. Germination markedly increased the contents of proteins, reducing sugars, free amino acids, vitamins, and phytochemicals such as phenolic and carotenoid compounds, with variation among different quinoa varieties. Relatively high levels of 5-methyltetrahydrofolate (5-MTHF) were found in 6-day-old quinoa sprouts, especially in the LL-1 variety (1747.25 μg/100 g DW), followed by QL-2 sprouts (1501.67 μg/100 g DW). Furthermore, we examined the relative expression of genes involved in the folate biosynthetic pathway during QL-2 germination. The expression of the ADCS gene was upregulated 28.31-fold in 6-day-old sprouts, greatly facilitating folate synthesis. Pterin synthesis genes regulate the biosynthesis and further accumulation of folate by controlling pterin metabolic flux. Overall, the 6-day-old sprouts were recommended as a functional food with nutritional value and health benefits in dietary supplements.