High-tunnel (HT) systems have been shown to effectively improve yields, fruit quality and profitability. In order to maximize returns on investment, HTs are frequently planted successively with both winter and summer cash crops and may include >2 crop cycles per year in some climates. The intense cultivation strategies used in HT systems necessitate increased tillage and nutrient demands posing challenges for soil health, environmental quality and long-term economic sustainability, particularly among organic growers. Seasonal rotations that incorporate fertility-building cover crops, such as legumes and other green manures, have the potential to build soil organic matter, improve crop yield and reduce applications of animal manure and/or compost. The economic impact of cover crop use in HT production systems poses important implications for organic growers. In this study, we present three partial budget analyses to quantify the economic benefits from a leguminous winter cover crop–tomato cash crop rotation in HTs across three regions. Data used in the economic analysis come from multi-year organic HT field trials in Kansas (2016–2019), Kentucky (2016–2019) and Minnesota (2016–2020). Direct financial benefits from hairy vetch (Vicia villosa) cover crop N credits were observed but not sufficient to offset the direct and indirect costs of the cover crop practice. A winter cover crop used in organic HT vegetable systems results in negative financial benefits to producers even with conservation incentive payments. These results highlight challenges for organic growers who are required under the USDA National Organic Program to incorporate soil building practices as part of their rotation schedule. The findings will also be of interest to policy makers as they refine cost-share offerings and programming to incentivize cover crop adoption as a conservation strategy.