The No-till system and organic fertilization combined can be a potential strategy to avoid nutrient leaching, as the soil structure plays a crucial role in retaining them. In this study, we evaluated the influence of different rates of a bio-fertilizer made of industrial organic waste (IOW) from a poultry slaughterhouse on the percolation and stocks of nitrate in disturbed and undisturbed soil samples collected from a subtropical no-till field in southern Brazil. In an incubation experiment, we performed a percolation experiment using lysimeters and simulated rainfall for 180 days and evaluated the remaining soil nitrate stock after the incubation period. We set up a completely randomized experiment with three replicates using four IOW rates (equivalent to 0, 2, 4, and 8 Mg ha−1) and two sample types: disturbed and undisturbed soils. Using the bio-fertilizer increased nitrate mineralization from 0.77 to 1.55 kg ha−1 day−1. Overall, the IOW application increased the amount of percolated nitrate, significantly influenced by the simulated rainfall (p < 0.01). The amount of water flushed through the lysimeters was significantly higher for the disturbed soils (p < 0.05, LSD test), suggesting that the loosened structure promoted a higher water flux. No differences were observed between undisturbed and disturbed samples for nitrate percolation, implying that the amount of nitrate in the liquid soil phase may be a more critical factor in determining nitrate leaching than the water flux. The disturbed samples presented significantly higher nitrate percolation with increasing IOW rates, regardless of precipitation. Stocks in the 0–5 cm depth were 6.6 kg ha−1 higher for undisturbed samples (p < 0.05, LSD test). This result suggests preserving the soil structure can significantly increase the nitrate stocks upon IOW application.