In order to guarantee the safety of genetically modified (GM) soybean crops, it is important to assess the potential toxicity of their expressed insecticidal proteins to non-target organisms. In the present study, the effects of the GM soybean Insulin-like Growth Factor (IGF), which is tolerant to the herbicide glufosinate, on plant-dwelling non-target insects and arachnids were evaluated in soybean agroecosystems. For comparison, the non-GM parental cultivar of soybean Gwangan-kong was used as a control. Data were collected in 2016 and 2017 via surveying at Ochang and Jeonju, Korea. In total, 13,031 individual insects and arachnids, representing 64 families in 11 orders, were captured during the study. Firstly, the results indicate that the GM soybean IGF did not negatively affect plant-dwelling non-target insects and arachnids. However, the numbers of captured individuals on both IGF and Gwangan-kong were higher at Ochang in 2017. The occurrence of insect pests, natural enemies, and other insects differed significantly according to region, region and survey year, and survey year, respectively. In addition, the dominance, diversity, evenness, and richness indices for the collected insects varied significantly among the regions and survey years regardless of soybean variety. The score from PROXSCAL multidimensional scaling using combined data showed that insects and arachnids in different natural environments were separated by their cultivation regions and years irrespective of soybean cultivars.