Stacked crop rotations and improved cultural practices have been used to control pests, but their impact on soil organic C (SOC) and crop yield are lacking. We evaluated the effects of stacked vs. alternate-year rotations and cultural practices on SOC at the 0- to 125-cm depth and annualized crop yields from 2005 to 2011 in the northern Great Plains. Stacked rotations were durum (Triticum turgidum L.)-durum-canola (Brassica napus L.)-pea (Pisum sativum L.) (D-D-C-P) and durum-durum-flax (Linum usitatissimum L.)-pea (D-D-F-P). Alternate-year rotations were durum-canola-durum-pea (D-C-D-P) and durum-flax-durum-pea (D-F-D-P). Cultural practices were traditional (conventional till, recommended seed rate, broadcast N fertilization, and reduced stubble height) and ecological (no-till, increased seed rate, banded N fertilization, and increased stubble height). Annualized biomass residue (stems and leaves) returned to the soil and grain yield were greater with D-C-D-P and D-D-C-P than D-D-F-P and greater with the ecological than the traditional practice. The SOC at 5 to 10 cm was lower with D-D-C-P than other crop rotations and lower with the ecological than the traditional practice. At 20 to 50, 50 to 88, and 0 to 125 cm, SOC was lower with D-D-F-P than D-C-D-P and D-F-D-P. Regardless of treatments, SOC declined linearly from 2005 to 2011. The SOC at 0 to 125 cm increased linearly with annualized crop yield (R² = 0.58, P ≤ 0.01). Stacked rotations reduced SOC storage and crop yield compared with alternate-year rotations. Ecological cultural practice increased crop yield with minimum impact on SOC compared with the traditional practice.