Producing certified organic crops in the dryland region of Eastern Washington is difficult. One main challenge is the lack of manure or other inexpensive sources of nutrients. As a result, growers must rely on legume-based rotations to meet the high nitrogen (N) needs of organic cereal crops. A long-term research study was initiated in 2003 in Pullman, WA, to evaluate nine rotation systems designed to transition dryland cereals from conventional to organic production. The systems ranged from intensive grain production to intensive legumes for forage or green manure, as well as systems with alternating cereal grains and legume green manure. Additional inputs from commercial organic fertilizers were included in some systems. The entire study was sown to certified organic spring wheat in 2006 and winter wheat in 2006-07. Samples of soil, cover crop, cash crop and weed biomass were collected annually from each system and tested for inorganic (soil) and total N (plant). Nitrogen inputs, net gains or losses, and soil inorganic N during the transition and certified organic phases were compared among rotations during and after the organic transition. Increasing the frequency and intensity of perennial or winter annual legumes managed as green manure or forage resulted in improved N fertility, certified organic wheat yields, and weed control than transition rotations with a higher frequency of spring cereals or spring peas. A better understanding of the N dynamics in each rotation system can assist in developing a comprehensive organic fertility and soil quality management plan for organic dryland crop production in the Pacific Northwest.