In order to achieve optimum N availability, organic and low-input farming systems require greater carbon inputs than conventional systems. The build up of soil organic matter is required to increase the potential for N mineralization. The diverse inputs of these systems impact nitrogen balance, storage in organic matter and loss. Organic (N from manure and winter legume cover crop), and low-input (N from reduced fertilizer and winter legume cover crop), farming systems are compared with conventional (N from fertilizer) systems at two long-term research experiments, 1989-1998 at the Sustainable Agriculture Farming Systems (SAFS) site, and 1993-2004 at the Long Term Research in Agricultural Systems (LTRAS) site, both at the University of California, Davis, to evaluate long-term fate of nitrogen fertilizer inputs. At each site, an evaluation of long-term N balance, storage and loss was conducted to assess the efficiency of each system. At both sites, the organic system had the greatest cumulative N input and N balance, while the conventional system had the highest N output. Although the organic system had the greatest cumulative N input, it showed the lowest N output of all the systems. Soil N storage at both sites was highest in the organic system. At the SAFS site, the organic system accumulated 901 kg N ha-1 over the period of the study, 3 and 11 times more than the low-input and conventional systems respectively. Similarly, at the LTRAS site, the organic system accumulated 685 kg N ha-1, while both the low-input and conventional systems lost over 300 kg N ha-1 soil N. At the SAFS site, there is a 4-year, five-crop rotation of tomato, safflower, corn, oats/vetch, and beans in organic, low-input, and one conventional system, while the other conventional system has a 2-year, two-crop rotation of tomato and wheat. Yields for both corn and tomato were comparable among all three farming systems. At the LTRAS site, each system has a intensive 2-year rotation of corn and tomato, with 3 replicates plots for each crop in a given year. Corn yields over the duration of the experiment were consistently higher in the conventional system, increasing over time. In the low-input and organic systems however, corn yields were consistently lower, decreasing over time despite consistently high levels of available soil N. Tomato yields in all systems followed similar trends with few significant differences among systems. Differences in corn yields between the two sites may be attributed to the variation in crop rotations, sequence of cover crops in the rotation, timing of corn planting among systems, and/or lack of synchronization between N mineralization and crop N demand. Our results indicate the challenge in optimizing crop N uptake in organic and cover crop based systems does not entirely rely on developing organic matter pools to increase N mineralization potential. Rather it is more important to influence the rate and timing of N mineralization. At the SAFS site, we found interactions among inputs (manure, cover crops and fertilizer) and soil organic matter influenced the rate of soil N mineralization. Future cropping systems should be designed to take advantage of these interactions to optimize N availability and to address issues of N use efficiency, sustainable N cycling and environmental impact.