Organic wheat and small grains are produced on relatively few acres in the inland Pacific Northwest. The objective of this study was to examine how the nitrogen (N) dynamics of cropping systems (CSs) produced during the transition phase impacted organic wheat yield and protein levels in the first 2 years of certified organic production. Certified organic spring wheat (SW) was produced in 2006 and winter wheat (WW) in 2007 following nine, 3-year transitional cereal, small grain and legume-intensive CSs. SW and WW following perennial alfalfa + oat/pea forage or 3 years of legume green manure tended to be more productive than wheat that followed systems that contained a small grain crop for at least 1 year during the transition. In addition to increasing soil N, well-established stands of forage and green manure provided adequate cover to reduce weed establishment prior to organic production. Effective weed control strategies were as important as increasing soil inorganic N levels for improving organic wheat production. Choice of crop type, cultivar and rotation is important in organic wheat systems and in this study, WW had better stand establishment, competition with weeds and higher overall yield than SW and would be a better-suited class of wheat for organic production in situations where spring weeds are the dominant problem. Regardless of CS or crop type, supplemental soil fertility (primarily N) during the organic production phase will be necessary to maintain high soil N levels and wheat yields in these dryland systems.