Background <p>Gamma-aminobutyric acid (GABA) can act as a signalling molecule and metabolite to increase plant salt tolerance. However, it is currently unclear which genes play a major role in the defence system under the sustained effects of salt stress and how different metabolic pathways work synergistically to regulate them. The transcriptomic data and metabolite analysis of 33 leaf samples from tomato (<i>Solanum lycopersicum</i> L.) seedlings under 175 mmol·L^− 1 salt stress revealed that the GABA + Na (GN) group presented strong salt tolerance.</p> Results <p>Amino acid synthesis, especially that of GABA, and some transporter-related genes played important roles in the GN group. Phenylalanine accumulation subsequently induced flavonoid biosynthesis via upregulating key genes involved in the flavonoid biosynthetic pathway, including the gene encoding enzyme protein PAL, 4CL, C4H, CHS and CHI. The molecular mechanism by which exogenous GABA enhances salt tolerance involves the induction of gene expression in pathways such as amino acid synthesis and transport and phenylpropanoid and flavonoid biosynthesis, increasing the content of intracellular small molecules with osmotic regulation function, thereby regulating ion transporter genes to accelerate Na⁺ transfer and maintain relatively stable osmotic pressure. <i>SlGAD1</i> overexpression alleviated salt stress by increasing the GABA content and the flavonoid biosynthesis pathway.</p> Conclusions <p>These findings provide direct evidence that exogenous GABA affects the phenylpropanoid and flavonoid pathways and ion transporters, which will be helpful for the development of GABA as an agent for inducing salt tolerance.</p>