Excessive use of nitrogen (N) in crop production has impacted ecosystems by contaminating soil and water. Management of N in agriculture is therefore of global concern. Sustainable agriculture systems that use leguminous cover crops such as hairy vetch (Vicia villosa Roth) to fix N and enrich soil organic matter by fixing carbon provide an alternative strategy. N signalling pathways were found associated with delayed leaf senescence and disease tolerance of hairy vetch-grown tomatoes. To test whether N in hairy vetch is the only contributing factor leading to these phenotypes, we designed a pot experiment in the field to analyse growth and gene expression in tomatoes, one set with soil overwintered without a cover crop (bare soil) and the other with soil overwintered with a hairy vetch cover crop including the vetch residue on the soil surface. Additionally, supplementary N fertiliser was also provided to aid distinguishing tomato responses to vetch from those to inorganic N. Tomato fruit yield, plant biomass and photosynthesis were higher in plants grown in vetch than bare soil. Tomato growth and photosynthesis metrics exhibited a parabolic response to inorganic N in bare soil, suggesting the potential for N toxicity in pots with the highest N rate. Vetch-grown tomato plants mitigated these effects and maintained elevated photosynthetic rates at high inorganic N levels. Vetch-grown plants also mitigated a decline in expression of several genes regulating nitrogen and carbon metabolism and upregulated the defence-related gene, osmotin, relative to plants grown in bare soil. Thus, some of the positive responses of tomatoes to a hairy vetch cover crop observed in the field seem mediated by physiological cues other than the additional N provided by the vetch cover crop.