The purported benefits of conservation tillage and continuous cropping in agricultural systems include enhancement of soil ecosystem functions to improve nutrient availability to crops and soil C storage. Studies relating soil management to community structure allow the development of bioindicators and the assessment of the consequences of management practices on the soil food web. During one year (December 2003-December 2004), we studied the influence of continuous cropping (CC), intermittent fallow (F), standard tillage (ST) and no tillage (NT) on the nematode assemblage and the soil food web in a legume-vegetable rotation system in California. The most intensive systems included four crops during the study period. Tillage practices and cropping pattern strongly influenced nematode faunal composition, and the soil food web, at different soil depths. Management effects on nematode taxa depended on their position along the coloniser-persister (cp) scale and on their trophic roles. At the last sampling date (December 2004), Mesorhabditis and Acrobeloides were positively associated with NH+4, while Panagrolaimus and Plectus were negatively correlated with certain phospholipid fatty acids (PLFA). Microbial-feeders were in general associated with both bacterial and fungal PLFA, microbial biomass C (MBC) by chloroform fumigation-extraction, total C and N, NH+4 and NO−3, and were most abundant in the surface soil of the NTCC treatment. Fungal-feeders were more closely related to PLFA markers of fungi than to ergosterol, a purported fungal sterol. Discolaimus, Prionchulus, Mylonchulus and Aporcelaimidae, in contrast, were associated with intermittent fallow and deeper soil layers. The organisms in the higher levels of the soil food web did not respond to the continuous input of C in the soil and a long recovery period may be required for appropriate taxa to be reintroduced and to increase. At the end of the experiment, each treatment supported quite different nematode assemblages and soil food webs.