Abstract We tested the hypotheses that management of the soil food web in the fall would enhance grazing on bacteria and fungi by microbivorous nematodes in the spring, consequently increasing N availability in cover-crop driven organic and low-input farming systems. The food web was manipulated by irrigating the dry soil of late summer and/or providing carbon sources. By creating conditions conducive for biological activity, we increased the abundance of bacterivore and fungivore nematodes in the fall and the following spring. Greater biological activity in the soil enhanced concentrations of mineral N available to the subsequent summer tomato crop. Mineral N concentration in the spring was associated with abundance of bacterivore nematodes, and with the corresponding Enrichment Index (EI) provided by nematode community analysis. Because environmental conditions that favour increase of bacterivore nematodes probably also favour other microbial grazers, including protozoa, the abundance of bacterivore nematodes may be an indicator of overall grazing activity and N mineralisation rates from soil fauna. Decomposition pathways in the spring, inferred from nematode bioindicators, were dominated by bacteria in plots that had been irrigated the previous fall while fungi were more prevalent in those that had not. The responses of omnivore and predator nematodes to our treatments were not consistent and there was no evidence that regulation of opportunist species by predators would be enhanced by the management practices imposed.