Malnutrition is one of the greatest challenges faced by humanity, which may be addressed by improving crop productivity to ensure food security. However, extensive use of synthetic fertilizers can lead to soil fertility degradation. This study highlights the potential of combining nanotechnology with biotechnology to enhance the germination rates of commercially important crop seeds. Bacterial biosurfactant extracted from a newly isolated Klebsiella sp. strain RGUDBI03 was used as a reducing and capping agent for the synthesis of zinc oxide nanoparticles (ZnO NPs) through a simple method. Extensive characterization of ZnO NPs through electron microscopic analysis showed well-dispersed, homogeneous NPs with a size range of 2–10 nm. High-resolution transmission electron microscopy (HR-TEM) images also revealed molecular fringes of 0.26 nm in single crystal ZnO NPs, with approximately 50% of the NPs exhibiting a size range of 2–4 nm. X-ray diffraction (XRD) results of ZnO NPs indicated the presence of (100), (002), (101), (102), (200), and (112) planes, confirming their crystalline nature. The presence of C = C–H, C = C, C–H, and C = C groups in both the bacterial biosurfactant and ZnO NPs, as depicted by Fourier-transform infrared spectroscopy (FTIR) spectra, confirmed the function of the biosurfactant as a reducing and capping agent. The nano-primed chickpea (Cicer arietinum) and rice (Oryza sativa) seeds showed an increase in water uptake rate, 89% and 92% respectively, compared to the control (73% and 44%), leading to an enhanced germination rate of 98% and 76%, compared to their respective controls (80% and 30%) under optimized conditions. Additionally, the nano-primed seeds exhibited higher levels of α-amylase activity in both seeds (0.37 mg/g for chickpea and 2.49 mg/g for rice) compared to the control. Notably, the ZnO NP priming solution exhibited no cytotoxicity on red blood cells and earthworms (Eudrilus eugeniae), indicating their non-cytotoxic and eco-friendly nature for future field trials.