Breeding spring wheat (Triticum aestivum L.) specifically for organic production has been suggested by producers and researchers alike. To investigate the effects of management systems on selected spring wheat breeding line performance in multi-location tests in the northern Great Plains, we used a randomly derived population of 79 F6-derived recombinant inbred lines (RILs) from a cross between the Canadian hard red spring wheat cultivar AC Barrie and the CIMMYT derived cultivar Attila. The population, including the parents, was grown on conventionally and organically managed land in 12 environments over 3 years. Direct selection in each management system (10% selection intensity based on grain yield) resulted in three lines being retained in each management system, over the multi-location testing. Gains from 10% selection for grain yield in a ‘selection’ year were 3.4 times greater in conventional multi-site yield trials than in organically managed trials. Two lines (BA 05 and BA 36) ranked in the top 10% of both the conventional and organic selection trial of 2005, remained ranked 2nd and 1st, respectively, under conventional management in multi-site yield trials. However, these lines ranked 53rd and 21st, respectively, for grain yield in the multi-site organic yield trials. Selected lines were each yield stable within the management system in which they were selected. Following replicated multi-location yield trials, three lines from the population (BA 02, 29 and 58) ranked within the highest 10% yielding lines in both conventional and organic systems. The results of this study suggest that selection differences occur across multi-location tests, and that selection for grain yield in organic systems should be conducted within organic systems. It is evident, however, that data obtained from conventional yield trials also has some relevance towards breeding for organic environments.