Plant-parasitic nematodes represent a substantial constraint on global food security by reducing the yield potential of all major crops, including soybean (Glycine max L.). The soybean cyst nematode (SCN) (Heterodera glycines I.) is widely distributed across all soybean production areas of the US, and is the major yield-limiting factor, especially in the Midwestern US. Double cropping (DC) is defined as producing more than one crop on the same parcel of land in a single growing season. Compared to conventional single annual crops, DC provides many advantages, including improving soil health, enhanced nutrient provisioning to plants, improvement of soil physical properties, control of erosion, decrease in tillage requirements, and enhanced profitability. In some double-cropping systems, soybean is planted following winter wheat (Triticum aestivum L.), and several reports suggest the potential of wheat to suppress SCN populations. Field trials were conducted from 2017 to 2018 to investigate the effect of wheat on SCN populations in double-cropping soybean. Nine fields with three levels of initial SCN populations (low, moderate, and high) were selected in Illinois. Wheat was planted in strips alternating with strips-maintained weed-free and under fallow over winter and early spring. Soybean was planted in all strips after the wheat harvest. Soybean cyst nematode egg densities were acquired at four time points: wheat establishment, post-wheat/pre-soybean, mid-soybean (R1 growth stage or beginning of flowering), and post-soybean harvest. Wheat strips reduced SCN egg densities compared with fallow strips at the R1 stage (−31.8%) and after soybean harvest (−32.7%). Field locations with noted SCN suppression were selected for a metagenomics study. The structure of fungal communities differed significantly between DC and fallow plots at soybean planting and after harvest (P<0.001). Fungal populations were affected by location at all sampling times and by treatments before planting and after soybean harvest. Several enriched fungal and bacterial taxa in wheat plots, including Mortierella, Exophiala, Conocybe, Rhizobacter spp., and others, were previously reported to parasitize SCN and other plant-parasitic nematodes. Knowing that phytocompounds with potential nematicidal activity are released via the root system of plants, we implemented a gas chromatography–mass spectrometry (GC-MS) pipeline to investigate the profile of phytochemicals in soil samples collected from these fields and reviewed the potential nematicidal activity of compounds with higher concentration in double cropping fields. A total of 51 compounds were detected with the GSMS analysis, 8 with unknown identification. Several compounds, including multiple fatty acids, had greater relative peak areas in double-cropping samples compared to fallow. This multi-approach study provides a better understanding of the mechanisms governing wheat's effect on SCN populations. Rather than a single mechanism, the suppression of SCN in soybean fields double-cropped with winter wheat is potentially linked to enriched microbial communities, increased populations of beneficial organisms, and higher concentrations of phytochemicals with nematicidal activity. This is the first study implementing metagenomics and GCMS to characterize soil microbial and chemical profiles in soybean fields double-cropped with winter wheat. Finally, a set of studies were conducted to evaluate the effect of two seed-applied succinate dehydrogenase inhibitors (SDHI) compounds, fluopyram and pydiflumetofen, on SCN population densities, plant injury, and plant growth. Next-generation sequencing was later employed to identify transcriptomic shifts in gene expression profiles of soybean seedlings treated with fluopyram and pydiflumetofen. Fluopyram reduced both SCN egg and cyst counts in comparison to pydiflumetofen and the untreated control. RNA expression patterns of seed treatments clustered by sampling time (5 DAP vs 10 DAP). Multiple DEGs identified in soybean seedlings treated with fluopyram are reported to be linked to systemic resistance, suggesting a role of systemic resistance on the suppression of SCN by fluopyram. The non-target inhibition of soybean succinate dehydrogenase genes by fluopyram may be the origin of the phytotoxicity symptoms observed and potentially the cause of the systemic resistance activation reported in the current study. To our knowledge, this is the first report of systemic resistance being activated by fluopyram in addition to the suppression of soybean succinate dehydrogenase (SDH) and ubiquinone oxidoreductase genes. This work helps to elucidate the mechanisms of suppression of SCN by fluopyram