Quinoa (Chenopodium quinoa Willd.) is a nutritionally complete pseudocereal containing all essential amino acids required by humans. To investigate the accumulation mechanism of γ-aminobutyric acid (GABA) during quinoa germination, we used quinoa cultivar M059 as experimental material, determined GABA contents at 12 h and 24 h of germination, and compared transcriptomic differences between these two time points.The results showed that the GABA content reached a peak of 24.47 μg/g at 24 h of germination, which was 2.27-fold higher than that at 12 h. Transcriptome analysis identified 1146 differentially expressed genes (DEGs), including 913 up-regulated genes and 233 down-regulated genes. GO enrichment analysis indicated 19 GO pathways closely related to GABA synthesis during germination. KEGG pathway analysis identified six metabolic pathways associated with GABA synthesis, among which the alanine, aspartate, and glutamate metabolism (ko00250) and arginine and proline metabolism (ko00330) pathways were highlighted as the core regulatory routes.The expression levels of the key genes CqGAD (LOC110718614) and CqALDH3H1 (LOC110709762) were up-regulated by 1.9-fold and 1.1-fold, respectively. Transcription factor analysis identified potential transcriptional regulatory relationships of key genes: CqSPL8 (r=0.77), CqWRKY24 (r=0.91), and CqWRKY6 (r=0.97) positively regulate CqGAD, while CqHSFC1 (r=-0.97) negatively regulates CqGAD. For CqALDH3H1, CqERF091 (r=0.89), CqWRKY24 (r=0.88), and CqTGA9 (r=0.91) positively regulate its expression, while CqABI4 (r=-0.91) negatively regulates it. Notably, CqWRKY24 serves as a common regulatory factor that positively regulates both CqGAD and CqALDH3H1. qRT-PCR results confirmed that the expression levels of CqSPL8(LOC110714232), CqWRKY6(LOC110720931), CqHSFC1(LOC110691034), CqERF091(LOC110693708), CqWRKY24(LOC110730454), CqTGA9(LOC110684250) and CqABI4(LOC110699305) were consistent with the transcriptome data.This study demonstrated that the efficient accumulation of GABA during quinoa germination is the result of the synergistic effect of the GAD-catalyzed glutamate pathway and the ALDH-mediated polyamine degradation pathway, and WRKY family transcription factors play a key regulatory role. The findings provide a valuable reference for elucidating the key metabolic pathways and molecular mechanisms underlying GABA accumulation during quinoa germination.