Soybean cyst nematode (SCN), Heterodera glycines, remains a major yield-limiting pathogen of soybean. Natural suppression of SCN exists and becomes increasingly attractive; however, ecological mechanisms leading to the suppressive state are rarely studied. A glasshouse experiment was performed to determine the effects of soil disturbance and biocides on nematode community and extracellular enzyme activities in the SCN-suppressive soil collected in 2007 and 2008. Soil disturbance was simulated by passing soil through a sieve (aperture 5 mm) and compared with no-disturbance (non-sieve) treatment. Composition of microbial communities was manipulated by applying captan (fungicide), streptomycin (bactericide), captan plus streptomycin, or no biocide. SCN egg population density, proportion of second-stage juveniles (J2) parasitised by fungi, nematode communities in the soil, and plant weight in each pot were determined 70 days after planting soybean. In addition, the activities of six selected hydrolytic and oxidative extracellular enzymes representing cellulase, chitinase, serine protease, collagenase and peroxidase were measured. Soil disturbance resulted in an increase in SCN egg population density and reduction in the proportion of J2 parasitised by fungi. Biocide treatments increased SCN egg population density and the proportion of J2 parasitised by fungi at the end of experiment. Values of nematode community diversity index decreased and dominance and maturity indices increased in the disturbed soil compared with the no-disturbance treatment. Biocide treatments reduced maturity index values exclusively. With soil disturbance, the activity of extracellular enzyme L-proline aminopeptidase activity declined to less than half of that under no-disturbance in 2007. This experiment showed that both bacteria and fungi were potentially involved in the soil suppressiveness to SCN: soil disturbance and biocide application may reduce natural soil suppressiveness that was potentially associated with soil nematode community diversity and microbial enzyme activities.