Recent advances in the microbial degradation of persistent organic pollutants have the potential to mitigate the damage caused by anthropogenic activities that are harmfully impacting agriculture soil ecosystems and human health. In this paper, we summarize the pollution characteristics of neonicotinoid insecticides (NNIs) in agricultural fields in China and other countries and then discuss the existing research on screening for NNI-degrading functional bacterial strains, their degradation processes, the construction of microbial consortia, and strategies for their application. We explore the current needs and solutions for improving the microbial remediation rate of NNI-contaminated soil and how these solutions are being developed and applied. We highlight several scientific and technological advances in soil microbiome engineering, including the construction of microbial consortia with a broad spectrum of NNI degradation and microbial immobilization to improve competition with indigenous microorganisms through the provision of a microenvironment and niche suitable for NNI-degrading bacteria. This paper highlights the need for an interdisciplinary approach to improving the degradation capacity and in situ survival of NNI-degrading strains/microbial consortia to facilitate the remediation of NNI-contaminated soil using strains with a broad spectrum and high efficiency in NNI degradation.