The adventitious presence of transgenic crops in wild plant populations is of ecological and regulatory concern. In this context, their effects on non-target, below-ground organisms are not well understood. Here, we introduced, at various frequencies, Bt-transgenic oilseed rape (OSR, Brassica napus) into wild mustard (Brassica juncea) populations in the presence and absence of the target herbivore (Plutella xylostella). The impacts on soil nematode and microbial communities were assessed in this system. There were no significant changes on the number of nematode genera and abundance in proportions of OSR with mustard. Nonetheless, the Shannon–Wiener and Pielou evenness index was lowest in plant stands containing 50% of Bt-transgenic OSR. Among treatments, there was no significant variation for culturable soil microbes. There was a positive association between foliar herbivory and the abundance of plant parasitic (PP) and cp-3 nematodes, whereas there was no association between herbivory and soil microbial populations. There was no direct effects of the presence of Bt-transgenic OSR in wild mustard populations on the rhizosphere nematode and microbial communities, whereas its indirect effects via aboveground herbivory might be important to consider for biosafety assessments. •We model an invasion process of transgenic Brassica napus into wild populations.•We examine changes of nematodes and microbial community in the invasion process.•Transgenic B. napus has no direct effects on nematodes and microbial community.•Above-ground herbivory influences rhizosphere ecology via plant responses.•The indirect effects of Bt B. napus on soil invertebrates should be evaluated.