Abstract Background Nitrogen (N) availability is crucial in regulating plants’ abiotic stress resistance, particularly at the seedling stage. Nevertheless, plant responses to N under salinity conditions may vary depending on the soil’s NH 4 + to NO 3 − ratio. Methods In this study, we investigated the effects of different NH 4 + :NO 3 − ratios (100/0, 0/100, 25/75, 50/50, and 75/25) on the growth and physio-biochemical responses of soybean seedlings grown under controlled and saline stress conditions (0-, 50-, and 100-mM L − 1 NaCl and Na 2 SO 4 , at a 1:1 molar ratio). Results We observed that shoot length, root length, and leaf-stem-root dry weight decreased significantly with increased saline stress levels compared to control. Moreover, there was a significant accumulation of Na + , Cl − , hydrogen peroxide (H 2 O 2 ), and malondialdehyde (MDA) but impaired ascorbate-glutathione pools (AsA-GSH). They also displayed lower photosynthetic pigments (chlorophyll-a and chlorophyll-b), K + ion, K + /Na + ratio, and weakened O 2 •− -H 2 O 2 -scavenging enzymes such as superoxide dismutase, catalase, peroxidase, monodehydroascorbate reductase, glutathione reductase under both saline stress levels, while reduced ascorbate peroxidase, and dehydroascorbate reductase under 100-mM stress, demonstrating their sensitivity to a saline environment. Moreover, the concentrations of proline, glycine betaine, total phenolic, flavonoids, and abscisic acid increased under both stresses compared to the control. They also exhibited lower indole acetic acid, gibberellic acid, cytokinins, and zeatine riboside, which may account for their reduced biomass. However, NH 4 + :NO 3 − ratios caused a differential response to alleviate saline stress toxicity. Soybean seedlings supplemented with optimal ratios of NH 4 + :NO 3 − (T3 = 25:75 and T = 4 50:50) displayed lower Na + and Cl − and ABA but improved K + and K + /Na + , pigments, growth hormones, and biomass compared to higher NH 4 + :NO 3 − ratios. They also exhibited higher O 2 •− -H 2 O 2 -scavenging enzymes and optimized H 2 O 2 , MDA, and AsA-GSH pools status in favor of the higher biomass of seedlings. Conclusions In summary, the NH 4 + and NO 3 − ratios followed the order of 50:50 > 25:75 > 0:100 > 75:25 > 100:0 for regulating the morpho-physio-biochemical responses in seedlings under SS conditions. Accordingly, we suggest that applying optimal ratios of NH 4 + and NO 3 − (25/75 and 50:50) can improve the resistance of soybean seedlings grown in saline conditions.