The synthesis of biological silicon nano-particles (Bio-Si-NPs) is an eco-friendly and low-cost method. There is no study focusing on the effect of Bio-Si-NPs on the plants grown on saline soil contaminated with heavy metals. In this study, an attempt was made to synthesis Bio-Si-NPs using potassium silica florid substrate, and the identified Aspergillus tubingensis AM11 isolate that separated from distribution systems of the potable water. A two-year field trial was conducted to compare the protective effects of Bio-Si-NPs (2.5 and 5.0 mmol/L) and potassium silicate (10 mmol/L) as a foliar spray on the antioxidant defense system, physio-biochemical components, and the contaminants contents of Phaseolus vulgaris L. grown on saline soil contaminated with heavy metals. Our findings showed that all treatments of Bio-Si-NPs and potassium silicate significantly improved plant growth and production, chlorophylls, carotenoids, transpiration rate, net photosynthetic rate, stomatal conductance, membrane stability index, relative water content, free proline, total soluble sugars, N, P, K, Ca2+, K+/Na+, and the activities of peroxidase, catalase, ascorbic peroxidase and superoxide oxide dismutase. Application of Bio-Si-NPs and potassium silicate significantly decreased electrolyte leakage, malondialdehyde, H2O2, O2•−, Na+, Pb, Cd, and Ni in leaves and pods of Phaseolus vulgaris L. compared to control. Bio-Si-NPs were more effective compared to potassium silicate. Application of Bio-Si-NPs at the rate of 5 mmol/L was the recommended treatment to enhance the performance and reduce heavy metals content on plants grown on contaminated saline soils.