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Applying phytotechnologies with energy crops on lands contaminated with trace elements provides cellulosic biomass and improves soil health. The process can be reflected in changes in the soil nematode community structure. This study assessed the nematode community composition of soil with <i>Miscanthus</i> grown with different agronomic practices. The research was conducted at Fort Riley, Kansas, USA, in soil with aged contamination by Pb at 1000 to 1500 mg/kg. The experimental design was a randomized complete block composed of four replications of five treatments: Control-undisturbed mixed plant cover and four conditions of <i>Miscanthus</i> growth, which consisted of No-till, Till (immediately before planting), Till + P, and Till + biosolids. Analysis of abundance, diversity, and community functional status indicators showed differential sensitivity of nematode taxa to agronomic treatments. Significant transformations in the nematode trophic group structure occurred under <i>Miscanthus</i> cultivation compared with the undisturbed mixed plant cover. Shannon and Pielou index response to agronomic treatments illustrated decreasing nematode community diversity with all <i>Miscanthus</i> agronomic conditions. However, agronomic practices led to increasing nematode community maturity, but those effects varied between spring and fall seasons. Increasing herbivores and omnivore-predators were the primary drivers of the observed changes in the nematode community due to planting <i>Miscanthus</i>. The nematode ecological structure indicators suggested that growth in Pb-contaminated land using different agronomical practices likely affects essential soil processes. More study is needed to define the effects of pre-plant tillage and amendments to soil nematode communities and <i>Miscanthus</i> yield over multiple growing seasons of this perennial crop.