Cover crops and compost application may influence soil quality and productivity of fresh-market tomatoes. The effects of hairy vetch (HV) (Vicia villosa Roth) and livestock compost on soil C and N stocks, N availability, and tomato yield were evaluated for 2 years in a plastic high tunnel. Averaged across years, soil C and N stocks increased in plots incorporating hairy vetch and compost more than in plots with no hairy vetch and compost. When compared with baseline stocks (initial soil C and N stocks before the initiation of the examination), soil C stock increased by 3%, 2.8%, 2.6% in the HV treatment, the compost treatment, and the HV and compost treatment, respectively. In contrast, a 1.85% loss of soil C stock was observed in a no HV and no compost (bare) treatment. Soil N stocks increased in all treatments, with the greatest increase in the compost treatment (26%) and the lowest in the bare treatment (9.3%). Averaged across sampling dates, the HV treatment exhibited the greatest soil N availability and nitrate levels in leaf petiole in both years, whereas the bare treatment exhibited the lowest soil N availability and nitrate levels in leaf petiole. HV + compost and compost treatments showed a similar influence on soil N availability, but HV + compost exhibited greater nitrate levels in leaf petiole than the compost treatment. The marketable and total yields were 10% to 15% greater in the HV and the compost treatments than in the bare treatment. N uptake was 17% to 38% greater in the HV treatment than in the other treatments. Because of unstable cover crop production in the northern region, a combined application of cover crops and compost may be one of the best practices to compensate for low cover crop biomass production by increasing organic matter input to the soil, thereby improving soil quality and tomato yield.