Due to the uncertain future of the soil fumigants most commonly used in the EU, there is a need to develop new integrated pest management programmes to control crop diseases. Different nematode management practices, such as solarisation and the use of ecological nematicides, including nematophagous fungi, are used to control populations of plant-parasitic nematodes, one of the most common pests affecting crops. The objective of this study was to determine the effects of organic (neem seed paste and a mixture of nematophagous fungi) and conventional (oxamyl and fenamiphos) nematicides on soil physical chemical properties, soil biodiversity and plant biomass. Such effects were investigated in two types of habitats: low diversity soils from an agricultural farm and high diversity soils from a natural vegetation area. The greater effect was observed with the neem treatment, which induced a large boost of dauer juveniles in the nutrient-depleted soil, while the same treatment induced an increase of populations of less opportunistic, generalist bacterivore nematodes in the pine forest soil, rich in organic matter. We have studied the effects of different biological and chemical nematicides on the whole soil nematode community through ecological indices and their relationship with plant biomass, but further research is needed to improve understanding of the effect of these products on nematode assemblages.