The bacterial strain Pseudomonas qingdaonensis BD1 and the clay mineral Illite have demonstrated individual potential in stress mitigation; however, their combined impact on soybean performance under salt stress are not fully understood. This study aimed to evaluate the combined application of BD1 and Illite in enhancing salt stress tolerance in soybean. The survival of BD1 was tested across a range of NaCl concentrations (0, 50, 100, 150, 200 mM) and Illite concentrations (0-7%), with maximum growth observed at 100 mM NaCl and 3% Illite. The treatments were applied independently, and the combined treatment of BD1 and Illite was most effective in mitigating the salt stress. Their co-application significantly enhanced the plant growth and photosynthetic efficiency under salt stress. This combination (BD1+Illite) also reduced oxidative stress by lowering hydrogen peroxide (H2O2) and malondialdehyde (MDA) levels, likely due to elevated antioxidant enzyme activity. Ion analysis revealed that BD1+ Illite reduced Na + accumulation by 26.7%, while increasing K+, Ca2+, Mg2+, and phosphorus uptake by 46.5%, 52.7%, 29%, and 28.7%, respectively. Additionally, their co-application decreased abscisic acid (ABA) and salicylic acid (SA) by 40% and 20.3%, respectively, whereas jasmonic acid (JA) increased by 44.4%, indicating a favourable hormonal shift. Enhanced accumulation of sugars, organic acids and amino acids further contributed to osmotic adjustment. Gene expression analyses revealed upregulation of GmCYP707A2, GmSALT3, GmLAX1, GmLAX3 and GmNHX1 and downregulation of GmNCED3, GmCLC1, and GmPAL1, supporting improved stress adaptation. In summary, while BD1 and Illite individually alleviated salt stress, their co-application resulted in the most effective and consistent improvement in salt stress tolerance in soybean plants primarily through enhanced antioxidant capacity, improved ion homeostasis, hormone regulation, and stress-responsive gene expression. Thus, their combined use represents a promising and sustainable amendment for agriculture in salt-affected environments.