The impacts of two organic soil amendments on nematode abundance, community structure and soil characteristics were studied in field grown tomatoes. We hypothesized that as the raw (labile form) and composted (non-labile form) manures differ in their chemical composition and effect on microbial activity. Also they will have different effects on soil properties and directly and indirectly affect nematode community structure. Experiments were conducted during 2001–2002 in Wooster, Ohio on a silt loam soil. Treatments [raw or composted dairy cow manure in 2001 and beef calf manure in 2002, and an untreated control] were arranged in a randomized complete block design. Amendments were applied in the spring at a rate estimated to deliver 95–100 kg N ha −1, and incorporated prior to planting. Soil samples were collected in the spring (before adding amendments) and autumn (after crop harvest) to determine nematode abundance, community structure and soil characteristics: Shannon–Weiner ( H′), Simpson ( λ), Pielou ( J′) and combined maturity indices were used to compare nematode community structure in amended and non-amended plots. Spring incorporation of both organic amendments increased the abundance of bacterial feeding, fungal feeding, omnivorous and predatory nematodes, but decreased plant parasitic nematode populations. Plots treated with raw manure had the lowest number of plant parasitic nematodes while increases in non-plant parasitic nematodes were similar in both treatments. Shannon diversity ( H′) and combined maturity (∑MI) indices of soil nematodes were reduced in plots receiving raw but not composted manure. Application of raw manure increased total organic matter, microbial biomass-N, potentially mineralizable-N and C over composted manure in 2001, while both raw and composted manure increased particulate organic matter in both years. The effect of raw and composted manure on community indices was different in 2001 and 2002. We found a strong negative relationship ( r = −82, p < 0.0001) between the abundance of non-plant parasitic and plant parasitic nematodes across all treatments and sampling times, thus supporting the utility of the ratio between non-plant parasitic and plant parasitic nematodes as a useful soil quality indicator.