Background Seed germination, including variations in internal physiological and biochemical indicators, as well as gene expression, has been extensively studied in various plant species. However, there is a lack of significant research attention on the germination mechanisms of quinoa. This study investigated the levels of starch, total amylase, soluble sugars, soluble proteins, glucose, fructose, sucrose, maltose, as well as hormones including ABA and GA₃ during the germination of quinoa seeds. Additionally, enzymatic activities involved in the synthesis and metabolism of ABA and GAs were measured, and transcriptional data at 4 h and 12 h were analyzed to elucidate the internal physiological changes occurring during quinoa germination. Result Physiological and biochemical indicators imply that the process of germination involves the enzymatic activity of amylase, which catalyzes the hydrolysis of starch and sucrose. This enzymatic action leads to an increase in the concentrations of soluble sugars, proteins, maltose, and glucose. The enzymes NCED, ZEP, and AAO are involved in the regulation of ABA synthesis, whereas GA₃ levels are modulated by the coordinated activity of GA20ox, GA3ox, and GA2ox. Quinoa seeds exhibit insensitivity to ABA, while GA₃ plays a significant role in promoting seed germination. Transcriptome revealed upregulation of starch and sucrose metabolism and the EMP pathway and TCA cycle were enhanced during seed germination. This study identified 15 crucial genes related to ABA, GAs, starch/sucrose metabolism, and EMP pathway in quinoa germination, via integrated analysis of differential expression, annotations, correlation, and indicator content. Conclusion This study investigated the dynamic changes in physiological, biochemical, and energy metabolism indicators during quinoa seed germination by measuring these indicators in conjunction with ABA, GA₃, and transcriptome analysis. Key genes involved in the regulation of quinoa seed germination were identified. The findings provide a foundational theoretical framework for understanding the intrinsic mechanisms underlying quinoa germination and preharvest sprouting.