<p>The unintended spread of genetically modified (GM) crops and introgression into wild relatives raises concerns about ecological impacts. In South Korea, CP4-EPSPS-containing <i>Brassica juncea</i> hybrids (GM-hybrid <i>B. juncea</i>) have been detected in natural ecosystems. However, the impact of these GM crops on ecology remains unclear. In this study, we aimed to investigate the potential effects of GM-hybrid <i>B. juncea</i> on the gut and fecal microbiomes of <i>Armadillidium vulgare</i>, a dominant decomposer in natural habitats and an ideal model organism for assessing the ecological impact of GM plant material. Leaf litter from wild-type and GM-hybrid <i>B. juncea</i> was collected from the field, and feeding experiments were conducted using <i>A. vulgare</i> under controlled conditions. Although no significant differences in survival rates or growth were observed between groups, microbiome analysis revealed significant changes in both bacterial and fungal community composition and functional profiles in the gut and feces of the GM-hybrid-fed group. Specifically, in the GM-hybrid-fed group, the proportion of intestinal <i>Plectosphaerella</i> (Glomerellales) increased. Additionally, the bacterial Shannon index decreased, whereas the fungal Shannon index increased. Microbial network analysis revealed distinct interaction patterns and GM-hybrid-specific modules. GM-hybrids may influence decomposer-associated microbiomes through indirect pathways. Such influences could affect ecosystem-level processes such as decomposition and nutrient cycling. This experimental framework can be extended to other crop-derived hybrids or applied to different ecological contexts, providing a valuable basis for future assessments of transgene impacts on ecosystem functions.</p>