Most studies addressing the ecological effects of Bt crops have focused on non-target effects during the crop growing cycle. Less information is available on the fate of expressed toxins in crop residue after harvest in a no-till production system. This research investigated the effects of four post-harvest management practices on the degradation rates of Cry proteins expressed in SmartStax field corn. Cry protein degradation expressed as growth inhibition of Ostrinia nubilalis larvae after harvest was measured by a feeding bioassay, and enzyme-linked immunosorbent assays were used to detect the presence of Cry proteins. Cry proteins retained significant levels of biological activity at crop senescence and were still present in corn residue for more than 20 weeks after harvest. Despite inconsistencies in treatment effects, the study demonstrated that post-harvest practices that increase soil-residue contact increase protein degradation, thereby reducing the period of exposure for non-target organisms.