Agro-residual valorization offers a sustainable route for enzyme bioprocesses, reducing reliance on conventional starch substrates. In this study, soy residue was evaluated as a feedstock for extracellular amylase production by Exiguobacterium qingdaonense. Multi-scale modeling approaches including response surface methodology, kinetic fitting, and Monte Carlo reliability analysis were employed to capture process robustness. The optimized operating window was identified at pH 6.0, 50 °C, and 0.15% soy residue under standard aeration, yielding a predicted activity of 12.8 U/mL with a half-life (t1/2) exceeding 10 h. Lineweaver–Burk and Hanes–Woolf plots revealed consistent kinetic parameters (Km ≈ 0.0161; Vmax ≈ 12.24 U/mL), while dual Arrhenius modeling indicated activation and deactivation energies of 152.8 and 166.5 kJ/mol, respectively. Sensitivity analyses demonstrated strong dependence of enzyme yield on substrate concentration and aeration, with quadratic and modified Monod fits (R² ≈ 0.94–0.95) validating predictive accuracy. Comparative substrate screening confirmed soy residue as superior to wheat bran, rice husk, and bagasse, supporting higher yields. Importantly, life cycle assessment revealed a reduced carbon footprint (0.03–0.04 kg CO₂e/1kU) under waste valorization scenarios compared to conventional corn starch baselines (0.05 kg CO₂e/1kU). Tornado sensitivity analysis highlighted enzyme yield and allocation factors as key drivers of climate impact mitigation. Overall, this integrated workflow demonstrates that soy residue not only sustains high amylase productivity but also enhances process reliability and environmental circularity. The findings underscore the potential of agro-residual valorization in advancing resilient, low-carbon bioprocesses for industrial enzyme production.