Climate change and water scarcity in arid agroecosystems necessitate optimized irrigation and fertilization strategies to sustain crop production and soil health. This study investigated the effect of irrigation regimes (Fc 70–70–70%, 70–80–70%, and 80–80–80%) and Rhizotorphin biopreparation on soybean (Glycine max (L.) cv. Orzu) growth during 2023–2024 growing seasons under typical meadow-gray soil conditions of the Fergana Valley, Uzbekistan. The experiment was conducted under three irrigation regimes (Fc 70–70–70%, Fc 70–80–70%, and Fc 80–80–80%), arranged without biotreatment (T1, T2, T3) and with biotreatment (T4, T5, T6), replicated three times in a factorial design structure. This study aimed to evaluate the interaction between irrigation regimes and biofertilizer application on soybean productivity cultivated as a second crop, while simultaneously enhancing soil health. The results demonstrated that soybean biomass increased with higher irrigation norms, whereas the highest yield and grain quality traits were achieved under the moderate irrigation regime combined with Rhizotorphin treatment (T5). Notably, the highest soybean grain yield (2.12 Mg ha-1) and quality were achieved under the 70-80-70% irrigation regime combined with Rhizotorphin treatment (T5). Additionally, water productivity (WP) was also maximized in T5 (0.88 kg m−3), followed by T4 (0.81 kg m-3), whereas excessive irrigation in T6 reduced efficiency despite high biomass accumulation. Treatments without biofertilizer (T1–T3) produced lower seed output (58.3–61.4%) and smaller seed size (141.8–143.9 g per 1000 seeds), with oil content ranging from 22.3–23.2% and protein levels between 38.4–43.6%. In contrast, biofertilizer treatments (T4–T6) consistently improved seed quality traits. Likewise, nitrogen (N), phosphorus (P), and potassium (K) content in plant tissues were significantly higher under the combined effect (T5). Overall, considering climate change concerns, especially in arid climates, the integrated use of optimal irrigation regime with biotreatment can enhance soybean grain yield, improve soil fertility, and promote both economic and ecological sustainability.