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Vegetable production area is growing rapidly world-wide, yet information on nitrogen (N) losses, greenhouse gas emissions, and input efficiency is lacking. Sustainable intensification of these systems requires improved understanding of how to optimize nutrient and water inputs for improved yields while minimizing N losses. In this study, a 3-year vegetable crop rotation spanning an intensification gradient is investigated in Kentucky, USA: (1) a low input organic (LI), (2) high tunnel organic (HT), and (3) conventional (CONV) system. The objectives were to (1) characterize soil mineral N pools and NO3--N leaching, (2) quantify CO2 and N2O fluxes, and (3) relate crop yield to global warming potential (GWP) caused by CO2 and N2O losses in these three vegetable production systems. HT maintained consistently higher soil NO3--N; the average NO3--N content during the entire rotations in HT was twice as high as in the CONV and three times as high as in the LI system. Key N loss pathways varied between the systems; marked N2O and CO2 losses were observed in the LI and NO3- leaching was greatest in the CONV system. The 3-year cumulative CO2 emission in LI was 50% higher than in the CONV and HT systems. Cumulative N2O emission over the 3-year vegetable rotations from the LI was twice as high as in the CONV system, whereas 60% more N2O was produced from the HT than from the CONV system. Yield-scaled GWP was greater in the LI for all crops compared to HT and CONV systems.