<p>Using saltwater in agriculture has emerged as a solution that may help to address the issue of water supply for agriculture in light of current climate change. On the other side, salinity has a major impact on crop yield, particularly sensitive crops, and may have long-term implications for soil sustainability. Therefore, this study aimed to test the potential impact of a salt-tolerant bacterium, “<i>Stutzerimonas stutzeri</i> PV248835” along with arbuscular mycorrhizal fungi in alleviating salinity stress in soybean plants, which is regarded as one of the most important economic plants in Egypt. Our results showed that the arbuscular mycorrhizal species could still colonize soybean roots under both salinity levels (50 mM NaCl and 100 mM NaCl), and the combined application of (AMF + <i>S. stutzeri</i>) was more pronounced in enhancing the mycorrhizal indices (F%, frequency; M%, intensity; and A%, arbuscular development) in the roots. Moreover, the count of bacteria in the soybean rhizosphere was enhanced due to the bioinoculant applications under salinity stress. Furthermore, using bioinoculants improves soybeans’ morphological parameters, photosynthetic-related pigments, and nutrient uptake (N, P, and K) significantly at <i>p</i> ≤ 0.05 under salinity stress. While bio-inoculation leads to reduced Na uptake and Na⁺/K⁺ ratio in plant tissues compared to the control plants. In addition, bio-inoculation activates the antioxidant defense system in terms of PPO, POX, and CAT activities, while reduced proline accumulation was observed. The findings suggest that applying a combined treatment of (AMF + <i>S. stutzeri</i>) is an environmentally friendly way to alleviate salt stress in soybean cultivation while also preserving soil sustainability.</p>