Soil disturbance, reduced crop diversity, and decreased residue in intensively managed systems can negatively impact soil biological communities and soil health. This study examined the impact of long-term (>20 years) low- (forest, grassland), medium- (diversified annual cropping), and high-intensity (annual cropping, frequently to potatoes) land-use on soil nematode communities and soil health in 59 sites across Prince Edward Island, Canada. Soil samples (0–15 cm) were collected at five locations per site and analysed for soil biological (nematode communities, respiration, soil organic matter, permanganate oxidizable carbon (POXc), soil protein), chemical (pH, N, soil N supply, extractable nutrients), and physical (bulk density, texture) properties. Soil pH and extractable nutrients were lowest in the low-intensity sites, while total C and C:N ratios were highest and decreased with increasing land-use intensity (low > medium > high). Soil respiration, POXc, and protein were lowest for high-intensity sites. Low-intensity sites had greater nematode Shannon diversity and richness, and higher maturity and structure indices than the medium- and high-intensity sites (p < 0.05), signifying a more structured nematode community. Nematode communities from the high-intensity sites were more degraded and had significantly higher basal indices compared to the low- and medium-intensity sites. At the trophic level, the low-intensity system had higher numbers of omnivores and lower abundance of bacterivores. These differences in nematode trophic composition may result in differences in ecosystem function, including nutrient cycling and biological control.